[ccp4bb] [ccp4] NAGging problem?

[MARTYN SYMMONS]

For my sins I am making figures of TLR structures. These are dimeric in 
activated forms and glycosylated. So I sort of assumed that the sugars would 
inherit the chain id of the polypeptide they are attached to. But then in 2Z7X 
(TLR1/2 heterodimer) when I coloured the gycolysation to fit with the chains it 
did not look right. Looking at the LINK record again I found the following:
LINK ND2 ASN A 199 C1  NDG A 901 1555   1555  1.45  
LINK ND2 ASN A 414 C1  NAG A 911 1555   1555  1.45  
LINK ND2 ASN A 442 C1  NAG A 921 1555   1555  1.45  
LINK ND2 ASN B  51 C1  NAG A 801 1555   1555  1.46  
LINK ND2 ASN B 163 C1  NAG B 811 1555   1555  1.45  
LINK ND2 ASN B 330 C1  NAG A 821 1555   1555  1.46  
LINK ND2 ASN B 429 C1  NAG A 831 1555   1555  1.45  
So only _one_ of the NAGs bound to chain B ends up getting a B chain id! I'm 
guessing this is because in the dimers the bulk of the sugar ends up closer to 
chain A rather than the chain B which it is attached to. 
And according the the RCSB "chain IDs for all bound moieties and waters are 
assigned based on their proximity (number of contacts) to the nearest 
polymer".(http://deposit.rcsb.org/depoinfo/download/dp.pdf section 4.4.1 Chain 
ID assignment ). So is this why these chains get switched? If so, I have to say 
that is crazy - surely the covalent bonds, detected when preparing the LINK 
description, should always take precedence? 
Maybe more reasonable treatment has been applied in some cases - but I would've 
hoped that there would be some consistency - and so maybe the rules need 
re-writing to remove these anomalies. 
I was only making a figure - but for sure someone will be trying to use the 
data for something more useful and quantitative. This sort of stuff will make 
their analysis difficult.
All the best
  Martyn 
Martyn Symmons
Cambridge

[ccp4bb] Post-doctoral and technician positions in membrane protein structural biology

[Liz Carpenter]

Dear all,
We have positions open for a post-doc and a technician to study the structure 
and function of the zinc metalloprotease, ZMPSTE24.


Ø  ZMPSTE24 is an integral membrane enzyme that is embedded in the inner 
membrane of the nucleus.

Ø  It is required for correct processing of nuclear lamins.

Ø  Failure of this process leads to premature ageing diseases such as 
Hutchinson Gilford Progeria syndrome.

Ø  We solved the structure of human  ZMPSTE24 and found it has a unique fold, 
forming a huge cavity inside the nuclear membrane (Quigley et al., Science, 
2013)

Ø  We plan to study how this enzyme cleaves lamins in two places and how errors 
in lamin or ZMPSTE24 lead to disease.

Ø  We will also study the structures of other enzymes involved in lamin 
processing and protein lipidation.

We are seeking a post-doc and technician with a background in membrane protein 
structure and/or function to join our dynamic multidisciplinary team in Oxford.
Informal enquiries can be addressed to 
liz.carpen...@sgc.ox.ac.uk

To apply for these posts please follow this link:
Post-doc:
http://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/116298-Postdoctoral-Scientist-Integral-Membrane-Protein

Technician:
http://www.ndm.ox.ac.uk/current-job-vacancies/vacancy/116393-Laboratory-Technician-Membrane-Protein-Production


Applications before 12.00 noon on the 17th of December for the post-doc 
position and the 19 December 2014 for the Technician position please.

[ccp4bb] Software Developer Position@EMBL, Hamburg (Svergun Group)

[margret]

Dear All,

I would like to inform you that a software developer position is 
available at the EMBL Hamburg Unit in the research group of Dmitri Svergun.
I attach a brief description of the Vacancy Notice below. Deadline for 
application is 12th January 2015
Further Detailed Information can be found under : 
http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=jj&id=53279&aid=15470 



*Software Developer, Reference HH_00075

* Applications are invited for a software maintainer for the SAXS 
software package ATSAS, a program suite for small-angle scattering data 
analysis from biological macromolecules. The ATSAS suite is a collection 
of 20+ applications, actively developed for more than 15 years by the 
SAXS group at EMBL-Hamburg. It is in use in more than a 1000 academic 
research institutes world-wide. The software maintainer for ATSAS shall 
further improve the internal processes and general user experience.


The successful candidate will work within the SAXS group in Hamburg  
that provides a stimulating work environment. This position also 
involves frequent contacts with international users of the software.



Regards
Margret Fischer
--

[ccp4bb] Senior Scientist and Senior Java Web Developer positions at RCSB PDB/UCSD

[Rose, Peter]

The RCSB PDB at UC San Diego seeks candidates with a track record of 
achievement in Structural and Computational Biology combined with strong 
Scientific Software Development expertise.

For details and direction to apply please follow this link:
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/contact/job_listings.html

For more information about UCSD, please visit http://www.ucsd.edu/. As part of 
the University of California, we offer a generous benefits package plus many 
educational opportunities.

Please contact Dr. Peter Rose at pwr...@ucsd.edu for 
more information about the positions.


Peter Rose, Ph.D.
Scientific Lead, RCSB Protein Data Bank (http://www.rcsb.org)
San Diego Supercomputer Center
University of California, San Diego

[ccp4bb] Postdoctoral position at EMBL Grenoble

[Marco Marcia]

Location:Grenoble, France
Staff Category:  Postdoctoral Fellow
Contract Duration:2 years
Reference Number:   GR_00072
*Closing Date: 4 January 2015*


*Job Description*
The European Molecular Biology Laboratory (EMBL) is one of the highest 
ranked scientific research organisations in the world. The Headquarters 
Laboratory is located in Heidelberg (Germany), with additional sites in 
Grenoble (France), Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).


EMBL is seeking to recruit a postdoctoral researcher to join the group 
of Marco Marcia at EMBL Grenoble. EMBL is a leading international 
research organization with a collaborative atmosphere. We are seeking to 
recruit an outstanding candidate with a strong interest in applying 
structural biology approaches to important biological problems. We focus 
on ribonucleoproteins formed by long non-coding RNAs and involved in 
transcription regulation.


*Qualifications and Experience*
The successful applicant should hold a Ph.D. and have a solid background 
in biochemical analysis of protein and/or RNA complexes. Experience in 
single particle cryo-electron microscopy and/or X-ray crystallography 
would be an advantage. The laboratory has excellent access to 
state-of-the-art equipment including the ESRF synchrotron and a Tecnai 
F20 Polara equipped with K2 direct electron detector. We welcome 
applications from candidates that are interested in working at the 
interface of cryoEM and X-ray crystallography. Motivation to work in a 
multidisciplinary and international environment is fundamental to this 
position.


*Application Instructions*
Please apply online through www.embl.org/jobs

*Additional Information*
EMBL is an inclusive, equal opportunity employer offering attractive 
conditions and benefits appropriate to an international research 
organisation. Please note that appointments on fixed term contracts can 
be renewed, depending on circumstances at the time of the review.



--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)476207634
phone (office): 0033-(0)476207759
fax: 0033-(0)476207199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/