[ccp4bb] Postdoctoral Position in Structure Function Studies of Membrane Proteins in Portland (Oregon)

[Francis Valiyaveetil]

PostdoctoralPosition in Structure-Function Studies on Transport Proteins
Apostdoctoral position is available in the Valiyaveetil group at Oregon 
Healthand Science University in Portland, Oregon. The Valiyaveetil group 
investigatesstructure and function of ion channels and transporters using a 
combination ofstructural biology, unnatural amino acid mutagenesis, 
electrophysiology andspectroscopy.  See references [ELife (2018), 7, 
doi:10.7554/eLife.36478; NatCommun. (2018), 9, 5055; PNAS (2019)116, 
15939-15946] for examples of recent research from the lab.  The group is a part 
of the Program inChemical Biology in the Department of Chemical Physiology and 
Biochemistry.
Theposition is suitable for a highly motivated candidate with a recent (less 
than1 year) Ph.D. in Biochemistry, Biophysics or a related discipline.  The 
candidate will investigate glutamatetransporters (and related transporters) 
using a combination of biochemical,spectroscopic and structural approaches. The 
candidate for this position should have prior experience in 
proteinbiochemistry.  Expertise working with eukaryoticmembrane proteins will 
be a plus.  The position providesthe candidate with a unique opportunity to 
enhance their skills in structural biology with expertise in protein 
engineering and functional studies.
TheValiyaveetil lab is well equipped to carry out structural and 
functionalstudies of ion channels and transporters. OHSU provides an excellent 
scientific environment.  

Portland is consistently rated as one of themost livable cities in the US.

Toapply send CV, a 1-2 page description of graduate research and future 
researchplans along with contact information for three references by email to: 
valiy...@ohsu.edu  

OHSU is an equal opportunity, affirmative actioninstitution. 

 




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[ccp4bb] Five-year Postdoc Position Available

[TUNG LE]

*Dear all,*

*We are looking for a structural biologist/biochemist for structural
studies of bacterial chromosome/plasmid segregation machinery. Please see
the advert below, and bring to the attention of anyone in your labs who may
be interested. Thank you very much.*

*Best wishes,*

*Tung Le*

*We are looking for a structural biologist/biochemist to join a 5-year
Wellcome Trust-funded project in the Le lab (John Innes Centre-Department
of Molecular Microbiology-UK **https://www.tunglelab.org/*
*).*

The chromosomes of all living organisms must be compacted nearly three
orders of magnitude to fit within cells. Moreover, DNA must be packaged in
a way that is compatible with a myriad of DNA-based processes, including
replication, segregation, transcription, repair, and recombination. This
challenge is particularly acute in bacteria as chromosome segregation
occurs concomitantly with DNA replication rather than being separated
temporally, as in eukaryotes. How chromosome organization and its
integration with biological processes are achieved in vivo remains poorly
understood. To fill this knowledge gap, our lab aims to:

1) Elucidate the molecular mechanisms underlying chromosome organization
and segregation

2) Unravel the relationship between spatial chromosome organization
(locally and globally) and important biological processes in the cell.

We are particularly interested in how the Structural Maintenance of
Chromosomes (SMC) protein and Partitioning proteins (ParA-ParB-*parS*)
interact with DNA to organize and segregate the bacterial chromosome.

The combination of structural biology, genetics, cell biology, and
genome-wide techniques (ChIP-seq and Hi-C) has proved to be very effective
in investigating SMC/ParB in our lab. In the long term, we aim to apply
similar approaches to investigate other classes of chromosome-structuring
proteins. The ultimate aim of our lab is to understand the integration of
actions of different classes of architecture proteins in organizing the
chromosome.

The candidate will join a diverse group of students, postdocs, and
scientists and work closely with Prof. David Lawson, the John Innes Centre
(JIC) X-ray crystallography platform manager (
https://www.jic.ac.uk/research-impact/technology-research-platforms/protein-crystallography/).
The JIC also has a FEI Talos F200C TEM for sample screening purposes.
Candidates willing to learn cryo-EM is welcomed.

.*Qualifications:*

· PhD in a relevant field

· Experience in protein purification and enzymology

· Experience in X-ray crystallography or cryo-EM.

· Experience with microbiology is desirable

· Experience with AFM or HDX-MS is desirable

· Organized and detail-oriented

· Enjoys collaborations and teamwork.

*To apply:*

Email tung...@jic.ac.uk with

· a cover letter that highlights your experience, contributions to
science, and interests

· CV

We prioritize inclusiveness in our team and encourage individuals from
diverse backgrounds, and individuals committed to promoting diversity,
equity, and inclusion, to apply.



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Re: [ccp4bb] coot is drawing the unit cell away from the modelled molecule

[Folmer Fredslund]

Aside from Paul's instructions on how to manually choose a different
location from inside *Coot *perhaps using the

http://achesym.ibch.poznan.pl/

server would be a good idea for setting a position on the molecule that
should be more objective


Hope this helps,
Folmer



man. 1. feb. 2021 14.51 skrev Paul Emsley :

> On 01/02/2021 13:23, leo john wrote:
>
> >
> > I am sure this issue might have addressed before,
>
> Correct.
>
> > but somehow I am not able to find it.
>
> That's because email is a terrible system for archiving structural biology
> information. An that goes doubly
> so for the Jiscmail archive.
>
> We should use something better.
>
> > After refinement when I open the structure in coot and draw the unit
> cell, I find that the modeled molecule
> > is not centered in the cell (unitcell.png)
> > Please suggest me a way by which I can get the molecule centered.
>
> Centre (using middle mouse click) on an atom in the symmetry-related
> molecule that you would actually like
> to be the "main" molecule, then Calculate -> Modelling -> Symm Shift
> Reference Chain Here.
>
> > I have a Bromo-phenylalanine in the sequence that I have modeled, but I
> get the red and green density around
> > Br atom (brphe.png). What can be the possible reason and how can I get
> rid of it.
>
> Tha looks right out of Dale's "Introduction to Maps" presentation. It's
> anisotropy. Thing about what you'd
> get if you subtract a gaussian sphere from a gaussian ellipsoid. You can
> either model it with anisotropic
> B-factor refinement (perhaps just that atom) or maybe split the residue by
> adding an alt conf.
>
> Paul.
>
> 
>
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[ccp4bb] Postdoctoral positions at the University of Texas Southwestern Medical School

[Yanhe Zhao]

Dear all,

On behalf of Prof. Nicastro,

The Nicastro lab (https://www.utsouthwestern.edu/labs/nicastro/) in the Cell 
Biology Department of UT Southwestern Medical School in Dallas is recruiting 
two postdoctoral fellows with experience in cell biology and/or structural 
biology to work in the field of cellular cryo-electron tomography.


Why join the Nicastro lab:

  *   We have access to state-of-the-art facilities and instrumentation 
(including two Krios electron microscopes, an Aquilos cryo-FIB and cryo-CLEM - 
see https://www.utsouthwestern.edu/labs/cemf/ - and a high-performance 
computing cluster).
  *   We are highly collaborative, and fellows can choose from a range of 
interesting projects (e.g. cytoskeletal assemblies, cilia, organelles, 
host-pathogen interactions, technical development and more).
  *   This is an exciting time to join the field of cellular cryo-electron 
tomography: cryo-focused-ion beam (cryo-FIB) milling allows imaging "slices" of 
organelles/cell/small organisms that were otherwise too large, correlative 
imaging allow better targeting of regions of interest, and hardware/software 
advances continue to increase the achievable resolution.

Qualifications:

Highly motivated and creative Ph.D., with interest in learning new imaging 
techniques to study biological processes. The candidate must be able to work 
independently, as well as demonstrate a strong commitment to team-based work. 
Prior knowledge in cryo-electron microcopy is not required.



Interested applicants should send their Curriculum Vitae and cover letter 
describing their motivation to apply for the position to: Daniela Nicastro 
(email: 
daniela.nicas...@utsouthwestern.edu)



UT Southwestern is an equal opportunity employer committed to diversity (for 
more information please visit 
https://www.utsouthwestern.edu/about-us/administrative-offices/equity-access/).



Best wishes,

Yanhe


Yanhe Zhao
Postdoctoral Researcher of Prof. Nicastro's Lab
Cell Biology
UT Southwestern Medical Center
NL05110G
5323 Harry Hines Blvd.
Dallas TX 75390-9039
yanhe.z...@utsouthwestern.edu




UT Southwestern

Medical Center

The future of medicine, today.



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[ccp4bb] PDRA position at the Rosalind Franklin Institute - glycosaminoglycan biosynthesis

[Liang Wu]

Dear all,
 
I’m looking for a PDRA to work with me at the Rosalind Franklin Institute, UK 
(www.rfi.ac.uk) to investigate the biological mechanisms of glycosaminoglycan 
biosynthesis, in particular heparan sulfate.  The job would particularly suit 
structural biologists interested in glycobiology.
 
This position is funded by the Wellcome Trust and available for 4 years.  
Further details and the application submission portal can be found here:
https://opportunities.rfi.ac.uk/vacancy/postdoctoral-research-associate-in-glycosaminoglycan-biosynthesis-434615.html
  
 
Please also feel free to email me for informal enquiries. 
 
Applications close 15th Feb.
 
Best wishes
Liang
 



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Re: [ccp4bb] coot is drawing the unit cell away from the modelled molecule

[Paul Emsley]

On 01/02/2021 13:23, leo john wrote:



I am sure this issue might have addressed before,


Correct.


but somehow I am not able to find it.


That's because email is a terrible system for archiving structural biology information. An that goes doubly 
so for the Jiscmail archive.


We should use something better.

After refinement when I open the structure in coot and draw the unit cell, I find that the modeled molecule 
is not centered in the cell (unitcell.png)

Please suggest me a way by which I can get the molecule centered.


Centre (using middle mouse click) on an atom in the symmetry-related molecule that you would actually like 
to be the "main" molecule, then Calculate -> Modelling -> Symm Shift Reference Chain Here.


I have a Bromo-phenylalanine in the sequence that I have modeled, but I get the red and green density around 
Br atom (brphe.png). What can be the possible reason and how can I get rid of it.


Tha looks right out of Dale's "Introduction to Maps" presentation. It's anisotropy. Thing about what you'd 
get if you subtract a gaussian sphere from a gaussian ellipsoid. You can either model it with anisotropic 
B-factor refinement (perhaps just that atom) or maybe split the residue by adding an alt conf.


Paul.



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[ccp4bb] Postdoctoral fellowship to study membrane protein structural biology

[Magnus Andersson]

Postdoctoral fellowship to study membrane protein structural biology


The Andersson lab at the Department of Chemistry at Umeå University, Sweden, is 
looking to recruit a postdoctoral fellow (2-year fellowship, funded by the 
Kempe foundation) to join our team to study ATP-dependent membrane proteins 
with a specific focus on regulation mechanisms and bacterial antibiotic 
resistance. We combine structural biology techniques ranging from cryo-EM, 
X-ray solution scattering, and cutting-edge time-resolved X-ray scattering to 
determine structures of high-energy states (see our 2020 publication in Science 
  Advances) – that are invisible to other structural biology techniques. So, if 
you’re interested in pushing the limits of structural biology - come join our 
team!


Qualifications

The required qualification is a doctoral degree in molecular biology, 
biochemistry, biophysics, structural biology, or a related field. The applicant 
must have practical experience and expertise of protein production and 
purification. Prior experience from working with membrane proteins, nanodiscs, 
and structural biology techniques, are considered merits. Good knowledge of the 
English language, both written and spoken, is required. A suitable candidate 
should also have good collaboration skills, a high degree of independence, and 
problem-solving analytical ability.

 
Application

The application should include:

- A cover letter stating why you want to join the lab and study membrane 
protein structural biology (maximum 1 pages). This letter must also contain 
your contact details. 

- A Curriculum Vitae including a list of peer-reviewed published articles

- Copies of doctoral degree certificate and other relevant degree certificates

- Name and contact information for two reference persons of which one should be 
your PhD supervisor

Send your complete application to: magnus.p.anders...@umu.se and make sure to 
use the subject line: “postdoc application Kempe”. Applications will be 
accepted until March 15. The top ranked candidates will be contacted within 
three weeks from the closing date for an interview. Starting date according to 
agreement. For more information, contact Dr. Magnus Andersson.


The Andersson lab is part of the Integrated Structural Biology community at 
Umeå University, consisting of 14 research groups that use, and have access to, 
high-field NMR, X-ray crystallography, world-class cryoEM, and high-performance 
supercomputing.

Webpage: https://www.biostruct.umu.se/principal-investigators/magnus-andersson/

 

#
Magnus Andersson, Associate Professor
Integrated Structural Biology
Department of Chemistry 
Umeå University

Email: magnus.p.anders...@umu.se
Phone: +46 720 837370 

Mailing address:
Umeå University
Department of Chemistry
KBC-building
SE-901 87 Umeå

Visiting address:
Linnaeusvägen 6




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