[ccp4bb] Help to fight COVID-19

[Pramod Kumar]

Dear Structure Biologists,

We have some significant expertise in stabilizing the membrane proteins 
and domains in different kinds of membranous environments such as 
liposomes (small and giant vesicles suitable for biochemical and 
electrophysiological analysis), nanodiscs and malic acid based polymers. 
We are highly proficient for working up to BSL2 level experiments. In 
this tough time of COVID-19 pandemic we would love to 
share/help/collaborate with our expertise to any lab/organization 
interested in developing any kind of fundamental study or therapeutics. 
Please just contact us and we would do our level best.



Pramod Kumar, Ph.D.

Postdoctoral research associate, Grosman Lab

Department of Molecular and Integrative Physiology

University of Illinois at Urban-Champaign.



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Error running Phaser-MR

[Gihan Ketawala]

Hi. 

I get this "INPUT ERROR: Erro interpreting Composition sequence" message when I 
try to MR in ccp4 Pherser MR. I've been using regular *.fasta file for the 
sequence. First, I thought the error coming from the changes I made to the 
*.fasta fill, but even when I'm using the original file straight from the PDB I 
still get the error. Any help you guys can give to point me in the right 
direction is highly appreciated.

Gihan

i.e. I'm getting the same error with Phenix-Phaser MR as well



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Michel Fodje]

In Ascoidea asiatica where CUG is translated as both Leu and Ser.
Mühlhausen S., Schmitt H.D., Pan K.T., Plessmann U., Urlaub H., Hurst L.D., 
Kollmar M. Endogenous stochastic decoding of the CUG codon by competing Ser- 
and Leu-tRNAs in Ascoidea asiatica. Curr. Biol. 2018; 28:2046-2057.

Perhaps, this is not a mutation at all but points to the origin of this virus.

/Michel.

From: CCP4 bulletin board  On Behalf Of Carter, Charlie
Sent: March 21, 2020 7:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: External: [ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19




Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is interesting.  Espeically since 
they are so far apart I expect this selective pressure might work in 

Re: [ccp4bb] CCP4BB vs COVID19

[Rigden, Dan]

Hi James


5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In fact, 
rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold similar to 
ORF7 (for which there is a structure; 1xak).


https://toolkit.tuebingen.mpg.de/jobs/2717885_1


I must say I got quite excited seeing that until I noticed this pre-print which 
tells the whole story very nicely, including that key position 84


https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1


Best wishes

Dan


From: CCP4 bulletin board  on behalf of Patrick Shaw 
Stewart 
Sent: 21 March 2020 15:41:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4BB vs COVID19


James, this isn't conventional structural biology, but may be of interest, and 
I haven't been able get any mainstream virologists to think about it.

The protein sequences are obviously of interest, but so are the RNA sequences 
at both ends of the Covid genome, which have conserved secondary structure.  A 
few years ago a paper came out suggesting that wild-type influenza has multiple 
"RNA thermometers", which may play an important role in the tropism of 
influenza.  Similar mechanisms may exist in other respiratory viruses, 
including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick


https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/

My paper in Medical Hypotheses 
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA 
thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced perturbations of 
secondary mRNA structures are associated with the cold-adapted 
temperature-sensitive phenotype of influenza A virus." RNA biology 9.10 (2012): 
1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of 
coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.



On Fri, Mar 20, 2020 at 10:59 PM James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in
this article: 

Re: [ccp4bb] CCP4BB vs COVID19

[Patrick Shaw Stewart]

James, this isn't conventional structural biology, but may be of interest,
and I haven't been able get any mainstream virologists to think about it.

The protein sequences are obviously of interest, but so are the RNA
sequences at both ends of the Covid genome, which have conserved secondary
structure.  A few years ago a paper came out suggesting that wild-type
influenza has multiple "RNA thermometers", which may play an important role
in the tropism of influenza.  Similar mechanisms may exist in other
respiratory viruses, including Covid.

My take on this, and the relevant papers, are below.

Good luck to everyone and stay well,

Patrick


https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/


My paper in *Medical Hypotheses *
http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf

Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA
thermometers." *FEMS microbiology reviews* 30.1 (2006): 3-16.

Chursov, Andrey, et al. "Specific temperature-induced perturbations of
secondary mRNA structures are associated with the cold-adapted
temperature-sensitive phenotype of influenza A virus." *RNA biology* 9.10
(2012): 1266-1274.

Yang, Dong, and Julian L. Leibowitz. "The structure and functions of
coronavirus genomic 3′ and 5′ ends." *Virus research* 206 (2015): 120-133.




On Fri, Mar 20, 2020 at 10:59 PM James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  

[ccp4bb] Fwd: [ccp4bb] CCP4BB vs COVID19

[Carter, Charlie]

Begin forwarded message:

From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>>
Subject: Re: [ccp4bb] CCP4BB vs COVID19
Date: March 21, 2020 at 8:07:53 AM EDT
To: James Holton mailto:jmhol...@lbl.gov>>

Brilliant post, James. Thanks so much!

I also find what you describe interesting, because of work done by a colleague, 
Manuel Santos, who showed that in fungi,

The CUG codon is decoded in vivo as serine and not leucine in Candida albicans
MAS Santos, MF Tuite
Nucleic acids research 23 (9), 1481-1486

I may be hallucinating, but I recall something to the effect that this genetic 
ambiguity also related to the ability of Candida to adapt to life in high 
concentrations of SDS.

Charlie

On Mar 20, 2020, at 6:59 PM, James Holton 
mailto:jmhol...@lbl.gov>> wrote:

You might think that as a structural biologist you won't be able to do much 
about COVID-19 anytime soon, but that is not true.  Yes, real-world 
therapeutics and vaccines take time, but we have already seen just how fast we 
can get started.  There are 21 PDBs already and some even have bound ligands.  
Good job Frank et al. BTW!  And my personal thanks to all of you out there who 
are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on the 
structural biology of SARS-CoV-2 as we move forward. It's a big virus, but 
there are not that many proteins in it.  If all of us independently do the same 
bioinformatics and literature searches and end up trying exactly the same thing 
in every lab all over the world, then that would be more than unfortunate.  To 
that end, I am personally interested on ORF8 for reasons I will go into below.  
Has anyone tried to solve it yet?  What happened?  Didn't express? Bad 
diffraction?  What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and labs 
dark while we shelter-in-place.  That doesn't mean our hands are tied.  We are 
still allowed to think. The fraction of the human race that has a snowball's 
chance in Hades of figuring out this bug is very very small.  Structure may be 
your main skill set, but you are still a biologist.  Do you know how to run a 
PCR machine?  Do you know how to pipette?  You might think that anybody can do 
it, but that is really not the case. Ever trained a new student on sterile 
technique?  How many days did that take?  Now remember that your student was no 
dummy and already studying biology.  Everyone reading this will make an 
excellent volenteer at the very least.  I'm not saying this to belittle the 
average human, only to say that we scientists, moving in the circles we do, 
often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The void 
left by the dearth and delay of test results has been filled with fear, and 
that is a big problem.  The tests, as defined, are straightforward, but also 
extremely regimented like any good laboratory protocol should be.  The US CDC's 
instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace 
supplies, in high-throughput mode and still valid?  Not just for clinical but 
for academic use?  I think more than a few people on this list could be 
regarded as experts in making a complex biochemical task faster, more 
efficient, high-throughput and nonetheless valid.  Yes, there are other people 
who do virus testing for a living, but right now they are all rather busy.  
Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in this 
article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for "T8517C" and you 
will find what I'm talking about.  The authors found two "types" of SARS-CoV-2. 
 They call them "S" and "L" because the only conserved amino acid change 
involved is S84L in ORF8.  The "S" type is believed to be the ancestor of "L".  
What is interesting is how tightly linked this mutation is to a silent mutation 
on the other end of the genome: the "L" type has a faster codon for Ser in 
ORF1.  Such tight coupling (r^2=0.945) means there must be significant 
selective pressure preventing both of these mutations occurring in the same 
virus at the same time.  That, I believe, is interesting.  Espeically since 
they are so far apart I expect this selective pressure might work in trans: as 
in a super-infection. That is, the S and L genome types may interfere with each 
other.

The authors fall short of claiming evidence of interference upon 
super-infection, and indeed they have already been criticised for calling "L" 
the "aggressive" type.  But it is still interesting and points a finger at ORF8.

ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch of 
60 residues.  This homologous region contains the S84L site (Val I544 in 5o32). 
 I had a quick look and appears to be a cavity-filling mutation 

Re: [ccp4bb] CCP4BB vs COVID19

[Boy]

The best way against COVID19 is staying at home, staying at home, and
staying at home.

Nothing else.

On Fri, Mar 20, 2020, 5:59 PM James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  That, I believe, is interesting.  Espeically since they are
> so far apart I expect this selective pressure might work in trans: as in
> a super-infection. That is, the S and L genome types may interfere with
> each other.
>
> The authors fall short of claiming evidence of interference upon
> super-infection, and indeed they have already been criticised for
> calling "L" the "aggressive" type.  But it is still interesting and
> points a finger at ORF8.
>
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a
> stretch of 60 residues.  This homologous region contains the S84L site
> (Val I544 in 5o32).  I had a quick look and appears to be a
> cavity-filling mutation to me.  Not very big, but maybe something could
> fit in there.  To be sure we'd need a structure of ORF8.
>
> Good luck to you all, and stay healthy.
>
> -James Holton
> MAD Scientist
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] CCP4BB vs COVID19

[Clemens Vonrhein]

Dear James,

On Fri, Mar 20, 2020 at 03:59:01PM -0700, James Holton wrote:
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a stretch
> of 60 residues.  This homologous region contains the S84L site (Val I544 in
> 5o32).  I had a quick look and appears to be a cavity-filling mutation to
> me.  Not very big, but maybe something could fit in there.  To be sure we'd
> need a structure of ORF8.

This is a very good example of why we all are trying to get raw
diffraction data deposited as soon as possible to the publication and
deposition of a structure. It highlights the potential benefit of
revisting some important structures right at the level of the raw
data. The paper says

  Diffraction data were collected at European Synchrotron Radiation
  Facility (ESRF) and Swiss Light Source at Paul Scherrer Institute
  (SLS-PSI). Diffraction data were processed by XDS and
  AIMLESS. Crystals of C3b–miniFH–FI exhibited space group P1 and
  diffracted to a resolution of 3.8 Å. However, the diffraction data
  was highly anisotropic. The data were therefore truncated to 4.2-Å
  resolution and rescaled using the Diffraction Anisotropy Server.

Obviously, that was state-of-the-art in 2015 (data collection) and
2017 (publication) - but maybe new methods could indeed do better on
this already existing structure if the raw data became
available. Maybe nothing will change in terms of structure quality and
(most importantly) structure interpretation ... who knows.

We've contacted the authors - who were very quick and extremely
helpful in providing us with raw images for some other deposited
project from their lab a few weeks ago, so expect and hope for a
similar response when/if the data can be located.

> Good luck to you all, and stay healthy.

Ditto!

Cheers

Clemens

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] CCP4BB vs COVID19

[Paula Salgado]

Same for Newcastle University, particularly our Faculty of Medical Sciences but 
colleagues and labs from across the University.

There are also several efforts to get scientists to help:

http://crowdfightcovid19.org/volunteers

Thanks to all those trying to help!

Paula



On 21 Mar 2020, at 11:53, David Briggs  wrote:


For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in
this article: 

Re: [ccp4bb] CCP4BB vs COVID19

[David Briggs]

For general interest,

The Francis Crick institute in London is offering facilities to public health 
England, and over 300 Crick scientists have volunteered to help with testing.

https://www.crick.ac.uk/news/2020-03-19_francis-crick-institute-offers-assistance-in-emergency-coronavirus-testing

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of David Waterman 

Sent: Saturday, March 21, 2020 11:12:36 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] CCP4BB vs COVID19

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to help 
fill the testing shortfall in the UK (see 
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers).
 This is a worthy initiative, if it is accepted (logistics are the main 
problem). The structural biology community is pretty good with this too. 
Perhaps there are some opportunities to help out here, for those who can still 
get to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton 
mailto:jmhol...@lbl.gov>> wrote:
You might think that as a structural biologist you won't be able to do
much about COVID-19 anytime soon, but that is not true.  Yes, real-world
therapeutics and vaccines take time, but we have already seen just how
fast we can get started.  There are 21 PDBs already and some even have
bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
all of you out there who are already hard at work on this.

I believe this forum is an ideal place to share information and ideas on
the structural biology of SARS-CoV-2 as we move forward. It's a big
virus, but there are not that many proteins in it.  If all of us
independently do the same bioinformatics and literature searches and end
up trying exactly the same thing in every lab all over the world, then
that would be more than unfortunate.  To that end, I am personally
interested on ORF8 for reasons I will go into below.  Has anyone tried
to solve it yet?  What happened?  Didn't express? Bad diffraction?
What?  Do tell.

Some of us, as you may have heard, are stuck at home, our beamlines and
labs dark while we shelter-in-place.  That doesn't mean our hands are
tied.  We are still allowed to think. The fraction of the human race
that has a snowball's chance in Hades of figuring out this bug is very
very small.  Structure may be your main skill set, but you are still a
biologist.  Do you know how to run a PCR machine?  Do you know how to
pipette?  You might think that anybody can do it, but that is really not
the case. Ever trained a new student on sterile technique?  How many
days did that take?  Now remember that your student was no dummy and
already studying biology.  Everyone reading this will make an excellent
volenteer at the very least.  I'm not saying this to belittle the
average human, only to say that we scientists, moving in the circles we
do, often forget that we have uncommon capabilities.

For example, I also believe we can be useful in assay development. The
void left by the dearth and delay of test results has been filled with
fear, and that is a big problem.  The tests, as defined, are
straightforward, but also extremely regimented like any good laboratory
protocol should be.  The US CDC's instructions for academic labs are here:
https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
My question is: how can this test be made faster, using more commonplace
supplies, in high-throughput mode and still valid?  Not just for
clinical but for academic use?  I think more than a few people on this
list could be regarded as experts in making a complex biochemical task
faster, more efficient, high-throughput and nonetheless valid.  Yes,
there are other people who do virus testing for a living, but right now
they are all rather busy.  Maybe if we put our minds to it we can help?

As for why ORF8.  I am basing my interest on the bioinformatics done in
this article: 
https://dx.doi.org/10.1093/nsr/nwaa036.
  Search for
"T8517C" and you will find what I'm 

Re: [ccp4bb] CCP4BB vs COVID19

[David Waterman]

Liz Tunbridge's lab at Oxford are offering PCR machines and expertise to
help fill the testing shortfall in the UK (see
https://www.wired.co.uk/article/coronavirus-uk-testing-key-workers). This
is a worthy initiative, if it is accepted (logistics are the main problem).
The structural biology community is pretty good with this too. Perhaps
there are some opportunities to help out here, for those who can still get
to their wet labs?

-- David


On Fri, 20 Mar 2020 at 22:59, James Holton  wrote:

> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical but for academic use?  I think more than a few people on this
> list could be regarded as experts in making a complex biochemical task
> faster, more efficient, high-throughput and nonetheless valid.  Yes,
> there are other people who do virus testing for a living, but right now
> they are all rather busy.  Maybe if we put our minds to it we can help?
>
> As for why ORF8.  I am basing my interest on the bioinformatics done in
> this article: https://dx.doi.org/10.1093/nsr/nwaa036.  Search for
> "T8517C" and you will find what I'm talking about.  The authors found
> two "types" of SARS-CoV-2.  They call them "S" and "L" because the only
> conserved amino acid change involved is S84L in ORF8.  The "S" type is
> believed to be the ancestor of "L".  What is interesting is how tightly
> linked this mutation is to a silent mutation on the other end of the
> genome: the "L" type has a faster codon for Ser in ORF1.  Such tight
> coupling (r^2=0.945) means there must be significant selective pressure
> preventing both of these mutations occurring in the same virus at the
> same time.  That, I believe, is interesting.  Espeically since they are
> so far apart I expect this selective pressure might work in trans: as in
> a super-infection. That is, the S and L genome types may interfere with
> each other.
>
> The authors fall short of claiming evidence of interference upon
> super-infection, and indeed they have already been criticised for
> calling "L" the "aggressive" type.  But it is still interesting and
> points a finger at ORF8.
>
> ORF8 has only one homolog in the PDB: 5o32 with 25% identity over a
> stretch of 60 residues.  This homologous region contains the S84L site
> (Val I544 in 5o32).  I had a quick look and appears to be a
> cavity-filling mutation to me.  Not very big, but maybe something could
> fit in there.  To be sure we'd need a structure of ORF8.
>
> Good luck to you all, and stay healthy.
>
> -James Holton
> MAD Scientist
>
>