[ccp4bb] Postdoctoral Research Associate in the Structural Biology of Supramolecular Protein Assemblies

[Owen Davies]

Dear all,

I would like to advertise a postdoctoral position that is currently available 
in my lab at the Wellcome Centre for Cell Biology, University of Edinburgh, UK 
(https://www.wcb.ed.ac.uk/research/owen-davies). This position is for an 
initial period of three years (with possibility to extend), to work on the 
integrative structural biology of the synaptonemal complex.

The synaptonemal complex is a supramolecular protein structure that assembles 
during meiosis to facilitate homologous chromosome synapsis and crossover 
formation. Its immense structure, of many micrometers in length, is formed 
through the combination of at least three unique self-assembling protein 
systems, which individually form lattice-like arrays, para-crystalline 
filaments and 'intermediate filament'-like fibres. This position aims to 
determine the molecular structure of the human synaptonemal complex and its 
constituent complexes through their reconstitution from recombinant proteins. 
This will be achieved through a cutting-edge structural biology approach, 
involving cryo-EM single particle reconstruction and tomography, structure 
solution of components by X-ray crystallography, solution biophysics (including 
X-ray and light scattering, and single-molecule biophysics), and the 
integration of experimental findings by advanced computational modelling of 
structures and assembly dynamics.
The post is funded by a Wellcome Senior Research Fellowship, and will be hosted 
in a well-equipped and well-funded lab, which includes the following:
Extensive biochemical equipment (including numerous Akta Pure systems, SEC-MALS 
etc)
Protein production and characterisation facility 
(https://www.ed.ac.uk/biology/research/facilities/edinburgh-protein-production-facility-eppf)
State-of-the-art biophysics equipment (including C-trap optical tweezers)
In-house TEM, SEM and newly upgraded cryo-EM facility 
(https://www.ed.ac.uk/biology/research/facilities/electron-microscopy)
Regular time on macromolecular crystallography and SAXS synchrotron beamlines 
at Diamond Light Source (https://www.diamond.ac.uk)
Regular cryo-EM time on Titan-Krios microscopes at Diamond Light Source 
(https://www.diamond.ac.uk) and Jeol microscopes at the Scottish Centre for 
Macromolecular Imaging 
(https://www.gla.ac.uk/researchinstitutes/iii/cvr/facilities/scmi/)
Local provision of high-performance GPU computation for cryo-EM, modelling and 
molecular dynamics

This position provides a unique opportunity for a highly enthusiastic applicant 
to perform transformative research through an integrative approach that is 
directed towards the new era of structural biology that address protein 
assemblies at a cellular scale. The successful candidate will lead this project 
(including several PhD students), and will be fully supported in applying for 
postdoctoral research fellowships within the lab, and independent research 
positions at the end of the postdoc. In suitable cases, at least part of the 
project, or a new project to be started during the employment, could be taken 
by the successful candidate as the basis for their future research career.
Please see the following manuscripts for examples of our previous work:
https://www.nature.com/articles/s41594-021-00636-z
https://www.nature.com/articles/s41594-018-0078-9
https://www.nature.com/articles/s41467-018-07794-7
https://www.science.org/doi/10.1126/sciadv.abb1660
https://elifesciences.org/articles/60175
Full publication list available at https://www.ed.ac.uk/profile/dr-owen-davies

The advert for the position is available via the following link:
https://www.jobs.ac.uk/job/CRX346/postdoctoral-research-associate-in-the-structural-biology-of-supramolecular-protein-assemblies

The application deadline is 6th September, and candidates should apply by 
following the 'apply' link on the above advert. Please feel free to contact me 
directly (owen.dav...@ed.ac.uk) for informal 
discussions and additional information.

Best wishes,

Owen.


Dr Owen Davies

Wellcome Senior Research Fellow

Wellcome Centre for Cell Biology

University of Edinburgh

Michael Swann Building

Max Born Crescent

Edinburgh

EH9 3BF
United Kingdom

The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh 
Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.



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[ccp4bb] SSRL/LCLS User's Meeting registration is open

[Mooers, Blaine H.M. (HSC)]

The SSRL/LCLS User's Meeting will be September 26-30, 2022.
It will be virtual again due to COVID, but the of the sessions will be recorded 
live.
Registration is free 
and open to all. We had about 1600 registrants last year.

We will have 27 workshops, 3 poster sessions, and 3 plenary sessions.
Distinguished plenary speakers include Drs. John Helliwell and Linda Young.

Although the registered attendees will be able to view the videos
at a later time, please do attend during the live sessions to participate in
the question and answer periods.

There will be several poster prizes. The BioXFEL prizes are not
limited to work done at LCLS. The 
deadline
 for the submission of
poster abstracts is September 9th.

Best regards,

Blaine Mooers on behalf of the SSRL/LCLS User's Meeting Organizing Committee
and the SSRL User Executive 
Committee
 and the LCLS User Executive 
Committee




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Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

[Jan Stransky]

Hi Matthew,

thanks for the thought.

Yes, I agree, that it is average whole lot of conformations. I am aware 
of  FEMs, it is great tool, but I got similar results as with Polder maps.


Modelling just the "main chain" and calling it Jeffamin, is also an 
option I was considering. It is part of the question, how to do properly 
for the PDB deposition. If I do just the Jeffamin "mainchain", it would 
be effectively PEG library, but not named as PEG. I think that would be 
confusing.


However, really treating it as aa residue with invisible sidechain is 
interesting option. Our lab consensus is to keep the atoms, but reduce 
occupancy to almost 0. I think, I could do that for the methyl groups in 
Jeffamin.


Best regards,

Jan


On 8/19/22 11:42, Matthew Snee wrote:

Hi

It is likely that your density is a consensus of multiple different 
jeffamines binding at different rotational orientations, so that at 
2.6A the methyl groups are essentially averaged out, and therefore the 
density may not exist to be found.


Phenix has a tool called "feature enhanced maps" which is designed to 
reverse the flattening of weak features, but I find its important to 
have the best possible phases (I.E most accurate model) before using it.


I suppose you could model jeffamine, and delete the methyl groups (I.E 
treat is like a residue with an unresolved sidechain).


Cheers

Matthew.

*From:* CCP4 bulletin board  on behalf of Jan 
Stransky 

*Sent:* 18 August 2022 10:37
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] Polymer ligand (Jefffamin) modeling in low 
resolution maps

Dear all,

we have a structure at not the greatest resolution (~2.6A) of which
crystal was grown in crystallization condition with Jeffamin. In the
maps, we see typical  PEG-like sausages. Jeffamin is basically a PEG
decorated with some methyl groups and it is terminated with amine groups.

Now, the question is how to interpret such blobs? To my understanding
the methyl decoration is not regular, and it is not obviously visible in
the maps. Nor is clear, if there is a contact to the amine group. When
we tried to put in PEG models as placeholders, it explains the density
fine, but the contacts  are nothing great, e.g. position of the oxygens
in the polymer is  not clear.

Calculating Polder maps does not clear things  up.

How would you deal with interpretation such maps?

Thank you for your ideas :-)

Jan



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Re: [ccp4bb] Polymer ligand (Jefffamin) modeling in low resolution maps

[Jon Cooper]

Hello Jan

Not a very helpful suggestion, but using rcsb's ligand-expo site I did find 
some structures of similar resolution in the PDB with jeffamine present. I 
don't know if looking at them would be helpful and you have probably done that 
already.

Sent from ProtonMail mobile

 Original Message 
On 18 Aug 2022, 10:37, Jan Stransky wrote:

> Dear all, we have a structure at not the greatest resolution (~2.6A) of which 
> crystal was grown in crystallization condition with Jeffamin. In the maps, we 
> see typical PEG-like sausages. Jeffamin is basically a PEG decorated with 
> some methyl groups and it is terminated with amine groups. Now, the question 
> is how to interpret such blobs? To my understanding the methyl decoration is 
> not regular, and it is not obviously visible in the maps. Nor is clear, if 
> there is a contact to the amine group. When we tried to put in PEG models as 
> placeholders, it explains the density fine, but the contacts are nothing 
> great, e.g. position of the oxygens in the polymer is not clear. Calculating 
> Polder maps does not clear things up. How would you deal with interpretation 
> such maps? Thank you for your ideas :-) Jan 
>  To 
> unsubscribe from the CCP4BB list, click the following link: 
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message 
> was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by 
> www.jiscmail.ac.uk, terms & conditions are available at 
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