[ccp4bb] Postdoctoral positions to study RNA-protein complexes and non-coding RNA in New York

[Alexander Serganov]

Postdoctoral positions to study RNA-protein complexes and non-coding RNA in New 
York

Postdoctoral positions are available immediately in the laboratory of Dr. 
Alexander Serganov at New York University School of Medicine. We are looking 
for enthusiastic, highly motivated and creative individuals with a strong 
interest in applying multidisciplinary approach and cutting-edge methodology to 
study RNA-mediated gene expression control. We are presently focusing our 
efforts on RNA-protein complexes and non-coding RNAs from bacteria and mammals, 
using structural (cryo-EM and X-ray), biochemical (including genome-wide) and 
biophysical methods. Research topics include transcriptional and translational 
control, mRNA modification, RNA degradation, and RNA-protein complexes in human 
diseases.
 
Candidates should hold a Ph.D. degree in structural biology, biochemistry, 
molecular biology, or related fields. Qualified candidates should have strong 
background in routine molecular biology techniques and protein purification. 
Good communication in English is expected.

The first position requires prior experience in genome-wide methods (RNAseq, 
CLIP, etc) or in vitro RNA studies. Projects will be primarily focused on 
genome-wide and in vitro characterization of RNA-protein interactions, with 
less emphasis on structural methods.

The second position requires experience in X-ray crystallography or cryo-EM and 
will primarily involve structural studies. 

The Serganov laboratory (www.serganovlab.com) is located on the NYU Langone 
campus at 31st Street and First Avenue in midtown Manhattan, New York, USA. 
Postdocs will benefit from the vibrant scientific environment and the 
outstanding School infrastructure that supports the most advanced technologies 
including robotic X-ray facility, cryo-EM facility with Titan Krios, genome 
center and over 20 other facilities. Postdocs will be involved in collaboration 
with leading groups and receive a competitive salary, excellent benefits, and 
subsidized housing. 
 
Interested applicants should submit a detailed CV, brief statement of research 
interests with description of previous research experience and contact 
information (email addresses and telephone numbers) of three references to Dr. 
Alexander Serganov at alexander.serga...@nyumc.org. Consideration of submitted 
applications will start immediately and continue until positions are filled.



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[ccp4bb] Postdoc position available in Indiana University School of Medicine

[Takagi, Yuichiro]

Dear Colleagues

We are looking for a highly motivated postdoctoral follow with a background in 
structural biology (X-ray crystallography, cryo-EM), to work on NIH-funded 
projects studying multi-protein complexes involved in eukaryotic transcription 
regulation. The information of this position is as follows:

Postdoctoral Fellow, Takagi Laboratory 
(https://medicine.iu.edu/research/faculty-labs/takagi/)
Department of Biochemistry and Molecular Biology
Indiana University School of Medicine

Who We Are:
My laboratory is interested in understanding the mechanisms of assembly, 
structure and function of large multi-protein complexes -“molecular machines” - 
involved in eukaryotic gene regulation, utilizing both cryo-EM and X-ray 
crystallography. We are particularly interested in the Mediator complex in both 
yeast and humans.

We believe that development and implementation of novel technologies is the key 
to unlocking the mysteries of how highly complex molecular machines (e.g. 
Mediator) function. Therefore, our overall research objective is two-fold: (i) 
development of novel technologies for studying multi-protein complexes, and 
(ii) application of these technologies to elucidate the structure and function 
of the Mediator complex.  In addition, we have developed a novel technology for 
producing pure preparations of difficult-to-express proteins and protein 
complexes, which has enabled several exciting ongoing projects with outstanding 
collaborators, including work on: plant RNA polymerases, DNA helicases, DNA 
repair complexes, RNA editing complex, and insulator complex.

 What We Offer:
1) State-of-the art protein and protein complex expression technologies (patent 
pending) enabling expression of difficult-to-express, problematic proteins and 
protein complexes

2) Accessibility to crystallization drop-setting robots, home X-ray sources, 
Synchrotron data collection at the Advanced Photon Source (APS) at Argonne 
National Laboratory (within a 3 hour drive from our lab), as well as 
electron-microscopy (EM) facility: Titan Krios, Talos Artica, and JOEL-FS3200

3) A one-on-one mentoring opportunity by which a postdoctoral fellow can learn 
the craft of designing research strategy, preparing compelling grant proposals, 
and paper-writing and presentation skills

4) The opportunity to work with multiple outstanding collaborators

Who Should Apply:
This position could be a great fit for you if:

- you have the expertise and experience in X-ray crystallography, and want to 
apply such skills toward structure determination of highly complex 
multi-protein complexes

- you are interested in learning and developing for the cutting-edge protein 
complex engineering and expression technologies

- you would like to extend your skill sets to cryo-EM

-you are self-confident and can communicate with the PI, other lab members, and 
collaborators with ease, and enjoy discussing research results and how to 
overcome technical challenges

- the specific research focus of our laboratory inspires you

- you love to gather information from the literatures  and helps generate 
creative ideas and technical solutions

- you relish working on technically challenging problems, which often require 
an extended persistent effort to crack


Job Description, Qualification, and Expectations:

Primary activities in this position include, but are not limited to:
- Expression and purification of the protein complexes for biochemical and 
structural studies
- Structure determination of the protein complexes by cryo-EM or/and X-ray 
crystallography
- Biochemical assays to characterize the recombinant protein complexes
- Providing intellectual contributions to the projects including writing 
manuscripts, fellowship application and helping PI for grant applications
- Ph.D. in structural biology (X-ray crystallography, cryo-EM) is strongly 
preferred 

If interested, please email a cover letter, CV, and two reference letters to 
ytak...@iu.edu 
Applications will be screened until a suitable candidate is found.  Indiana 
University is an equal opportunity/affirmative action employer.







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Re: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

[John Berrisford]

Dear Lucas

You may want to look at credo
http://marid.bioc.cam.ac.uk/credo
We (PDBe) are working on integrating this into both our website and API. 

John
PDBe

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lucas
Sent: 29 October 2018 13:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Parseable residue-ligand and/or residue-nucleic acid 
interaction database?

Just so that we don't reinvent the wheel: is there any database or webservice 
on which one can parse the list of residue-ligand interactions for the entire 
PDB? I'd like to programmatically obtain information such as "in PDB 3hdl the 
Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the nucleic 
acid chain B". I know this information is available through pdbsum via 
ligplot/nucplot, but I'm unaware if it is possible to download the entire 
interaction database and if it is parseable.



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[ccp4bb] Parseable residue-ligand and/or residue-nucleic acid interaction database?

[Lucas]

Just so that we don't reinvent the wheel: is there any database or
webservice on which one can parse the list of residue-ligand
interactions for the entire PDB? I'd like to programmatically obtain
information such as "in PDB 3hdl the Calcium 306 is in contact with
Asp223 or in PDB 5gjb Arg388 is in contact with the phosphate in the
nucleic acid chain B". I know this information is available through
pdbsum via ligplot/nucplot, but I'm unaware if it is possible to
download the entire interaction database and if it is parseable.



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[ccp4bb] Postdoc position in Structural Biology of Membrane Proteins at EMBL Hamburg

[Loew Christian]

Dear all,

We're currently looking to hire a postdoctoral researchers with a  
background in X-ray crystallography to join our research team at EMBL  
Hamburg.


Our group utilizes structural and biochemical approaches to  
characterize the dynamics, structure and regulation of nutrient  
transport proteins.


For more information, please see:
https://www.embl.de/jobs/searchjobs/index.php?ref=HH00154=1[]=0[]=0

Application deadline is 2nd December 2018.



Regards,

Christian Loew








Christian Löw, Dr.
Group Leader
Centre for Structural Systems Biology (CSSB)
EMBL Hamburg c/o DESY
Notkestraße 85
Building - 15 Room O2.205
22607 Hamburg
Germany

phone: +49(0)408998-87570
email: christian.l...@embl-hamburg.de



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[ccp4bb] Reminder - Travel bursaries for CCP4 Study Weekend 2019 - deadline for applications this Wednesday

[Karen McIntyre - UKRI STFC]

Travel bursaries are available for students and young Post-docs from non-UK 
labs to come to CCP4 Study Weekend 2019.

Deadline for applications is Wednesday 31st October 2018 i.e. this Wednesday!

For more info see http://www.cvent.com/d/sgq8q6/1K?cpc=N7N8SK89V8N

Regards

Karen McIntyre
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax +44 (0) 1235 56 7720

[*] @ccp4_mx

STFC is part of UK Research and Innovation
For more information visit https://stfc.ukri.org/

[cid:image002.png@01D46220.A8C3B260]

**Please note that I only work part-time until 1.30pm**




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