[ccp4bb] Postdoctoral position at the Ohio State University

[Krishna Chinthalapudi]

Dear All,



Applications are invited for a joint postdoctoral scientist position in the
laboratories of Dr. Sarah Heissler and Dr. Krishna Chinthalapudi at the
Ohio State University. The research project focuses on understanding the
role of myosin motors and cytoskeletal proteins in health and disease. We
combine state-of-the-art structural biology approaches including cryo-EM,
and X-ray crystallography with biochemical, biophysical, and cell
biological methods to investigate the structure and function of myosin
motors and their regulation by cytoskeletal proteins.



Our laboratories are equipped with state-of-the-art instrumentation for the
proposed studies and have generous access to a Titan Krios G3i Cryo-TEM
equipped with a bioquantum imaging filter and a K3 direct electron
detector, imaging phase plates, STEM/TEM tomography, and an image spherical
aberration corrector. In addition, our labs have access to a Glacios with a
Falcon III detector and a Ceta-D camera for MicroED analysis at the
world-class Center for Electron Microscopy and Analysis (CEMAS) at the Ohio
State University.



Candidates must have a Ph.D. degree and strong practical experience in
structural biology. Experience in molecular biology techniques, structural
biology, and/or high-resolution imaging are desirable.



To be considered for this position, please email your curriculum vitae, a
short cover letter with research experience and interests, and contact
information for three references to Sarah Heissler (sarah.heiss...@osumc.edu)
and Krishna Chinthalapudi (krishna.chinthalap...@osumc.edu).



Best,

Krishna



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[ccp4bb] ALS Webinar April 10th

[Paul Adams]

Dear Colleagues,

  A reminder that we will be hosting a webinar (registration link below) that 
provides information for the synchrotron structural biology user community 
about accessing the resources at the Advanced Light Source in Berkeley. This is 
timely because of the imminent closure of the Advanced Photon Source for a year 
for their upgrade. Synchrotron capacity for biosciences research will be 
significantly impacted, and we want to be sure that the community has 
information about alternative facilities during the APS dark time. 


http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10th-2023/

  The webinar will cover capabilities at the beamlines in macromolecular 
crystallography, small angle X-ray scattering, and X-ray footprinting, as well 
as information on how to apply for beamtime. While the webinar is of most 
relevance to the US research community, we welcome participation by anyone who 
is interested. 

  Cheers,   
Paul

--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL 
(https://biosciences.lbl.gov) 
Principal Investigator, Computational Crystallography Initiative, LBL 
(http://cci.lbl.gov) 
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org) 
Principal Investigator, ALS-ENABLE, Advanced Light Source 
(http://als-enable.lbl.gov) 
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) 
Adjunct Professor, Department of Bioengineering, UC Berkeley 
(http://bioeng.berkeley.edu) 
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley 
(http://compbiochem.berkeley.edu) 

Building 33, Room 250
Building 978, Room 4126
Building 977, Room 268
Tel: 1-510-486-4225
http://cci.lbl.gov/paul 
ORCID: -0001-9333-8219

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345 
Berkeley, CA 94720, USA.

Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
--



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[ccp4bb] Staff Scientist position at EMBL, Grenoble

[Jose A. Marquez]

Dear Colleagues,

Please, feel free to pass along to anyone that might be interested.

*Staff Scientist Position at EMBL, Grenoble*

EMBL is seeking to recruit a Staff Scientist in the Marquez team at the 
EMBL Grenoble unit. The Marquez team operates the High Throughput 
Crystallization Laboratory (HTX Lab) and has a strong focus on 
technology and methods development in macromolecular crystallography 
(CrystalDirect™, CRIMS, Online Crystallography), particularly in the 
area of fragment screening and structure-based drug design. They work 
closely with the EMBL instrumentation and synchrotron diffraction teams 
and apply these technologies to provide services to the wider scientific 
community and for their own research. The HTX lab cooperates in the 
operation of the ESRF MASSIF1 beam line, run by the EMBL - ESRF joint 
structural biology group, where the CrystalDirect technology has been 
recently implemented.


See details and the full job description at: 
https://www.embl.org/jobs/position/GR00203


Applications should be submitted through the www.embl.de/jobs/ portal.

*Deadline for application is April 23rd *.

For questions concerning this position please contact Jose  A. Marquez 
(marq...@embl.fr)


Best regards

Jose A. Marquez

_

Jose A. Marquez Ph.D.
Team Leader, Head of the Crystallization Facility
EMBL Grenoble Outstation
Postal address: European Molecular Biology Laboratory
71, Avenue des Martyrs
CS 90181 38042 Grenoble Cedex 9, France
Delivery address: European Molecular Biology Laboratory
71, Avenue des Martyrs
38000 Grenoble, France
Phone +33 (0)476 20 74 25
Fax. +33 (0)476 20 71 99

https://www.embl.org/groups/marquez/
https://www.embl.org/services-facilities/grenoble/high-throughput-crystallisation/
https://htxlab.embl.fr/
_



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[ccp4bb] PDRA position at the Rosalind Franklin Institute

[Wu, Liang (RFI,RAL,-)]

Dear colleagues,

I have a position for a postdoc at the Rosalind Franklin Institute, UK – 
closing soon 10th April.

The idea is to get someone (bio)chemically minded to look at protein labelling 
to aid cryoET imaging of glycosylation pathways inside Golgi complexes.  Would 
suit someone experienced in biochemistry or chemistry who wants to apply their 
skillset to living cells.

If you are interested, or if you know of anyone, please could you pass along 
this link 
https://opportunities.rfi.ac.uk/vacancy/pdra-in-situ-structural-biochemistry-517534.html

Thanks
Liang


--

Liang Wu
Group leader
Wellcome Trust Sir Henry Dale Fellow
Rosalind Franklin Institute
Harwell Campus
OX11 0FA




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[ccp4bb] PLEASE RESPOND – Request for support for the 2024-2028 CCP4 grant application for funding through the BBSRC UK

[Eugene Krissinel - STFC UKRI]

Dear All,


CCP4 asks you to support the 2024-2028 CCP4 grant application for funding 
through the BBSRC by signing on

the following web page:


https://forms.office.com/e/Abkb8fkHJx


Please express your support for the valuable resource that benefits the whole 
community.


Further details are appended below and in the attached document.


Many thanks,


Eugene Krissinel on behalf of Ivo Tews, CCP4 Chair.


Request for support for the 2024-2028 CCP4 grant application for funding 
through the BBSRC


Dear colleague,

We are writing to ask for your support for the scientific proposal we are about 
to submit to the BBSRC on behalf of CCP4 this month, that will deliver 
methodology to advance macromolecular crystallography. Collaboration partners 
in this proposal are the Universities of Liverpool, Newcastle, Southampton, 
York, the LMB Cambridge, STFC laboratories at RAL, and the Diamond Light 
Source. The core scientific support by BBSRC grants has been central to the 
success of CCP4 and has underpinned our ability to raise additional funds 
through commercial licences that support maintenance and distribution of the 
software and the user community.

Over the past year, CCP4 has collated ideas to define the current scientific 
challenges we need to address. The CCP4 Executive selected the strongest 
proposals, sharing and discussing them with the community at the Working Group 
1 meeting at the CCP4 study weekend earlier this year. Important new trends 
accelerate and enrich structural biology. The new-generation of machine 
learning computational models have a major impact – allowing us to use these 
models in our science and to solve new structures. The exponential growth of EM 
depositions complements macromolecular crystallography, providing many 
structures of membrane proteins and macromolecular complexes.

Your support underlines the central role that macromolecular crystallography 
continues to play in basic and translational bioscience, delivering the 
throughput and resolution needed for drug discovery and chemical probes, 
experimentally validating and improving computational models, and ideally 
complementing the strength of cryo-EM. The scientific objectives in the 
proposed work packages (WPs) build on the outputs of previous grants to deliver 
novel science and tools to transform the utility, throughput and accuracy of 
macromolecular crystal structure:


  *   to develop a theoretical framework to support the multi data - multi 
model nature of modern structural studies and enable joint refinement and 
description of the dynamic behaviour of macromolecules (WP1/WP2 - Diamond 
Source, the LMB Cambridge, and the Universities of Southampton and York);
  *   to generate novel tools for exploiting electron diffraction from 
macromolecular crystals (WP3 - STFC laboratories at RAL);
  *   to integrate exciting developments in AI to apply deep learning based 
predictions of contacts and distances, in particular for complexes and RNA 
targets (WP4 - Liverpool University).

We ask you to endorse our application by signing up on a form at 
https://forms.office.com/e/Abkb8fkHJx your email, your affiliation, and your 
position (PI, Technical staff, PDRA, PhD, undergraduate, or other). We will use 
the information to generate statistics that will be included with this 
application to the BBSRC (and no other purpose).

If you are a PI, we additionally ask you to send a letter of support directly 
to the CCP4 Chair (ivo.t...@soton.ac.uk). Letters of support must be received 
by the 17th of April.

With many thanks in advance for your time and support.

Ivo Tews
CCP4, Chair

The Collaborative Computing Project 4 was established in 1979 and continues to 
underpin world class macromolecular structural science in the UK. Effective use 
of data collected at synchrotron, XFEL and electron microscopy facilities is at 
the heart of the project’s mission. User communities benefiting from such 
research include academics as well as industrial users. At the interface of the 
two, CCP4 enables discoveries that underlie vaccine and therapy discovery 
(including, e.g., SARS-CoV-2) and may equally be applied to tackle modern 
challenges such as adaptation to climate change, biotechnology, or public 
health.





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CCP4_2024-28_CommunitySuppor.pdf
Description: CCP4_2024-28_CommunitySuppor.pdf

[ccp4bb] Removal of ls-lR index file from the PDB archive

[David Armstrong]

Dear PDB-l,

With continuing growth of the PDB archive, the size of the file that 
lists all directory contents (currently 
https://files.wwpdb.org/pub/pdb/ls-lR) will become a challenge for long 
term maintenance. wwPDB plans to remove this file from the PDB archive 
at 00:00 UTC on July 12, 2023. We strongly encourage users to utilize 
files previously announced that containing the same data 
(https://files.wwpdb.org/pub/pdb/holdings/).


These inventory data files offer a quick overview of data in the 
archive. These files are in the extensible JSON format, and can be found 
under the new /pdb/holdings/ archive tree.


The inventory lists provided include:

 * all_removed_entries.json.gz: a list of obsoleted PDB entries
   including information for entry authors, entry title, release date,
   obsolete date, and superseding PDB ID, if any.
 * current_file_holdings.json.gz: a list of released PDB entries and
   the file types present for each in the PDB Core Archive (e.g.
   coordinate data, experimental data, validation report).
 * obsolete_structures_last_modified_dates.json.gz: a list of obsoleted
   PDB entries with  information about the most recent modification
   date of the PDBx/mmCIF file.
 * refdata_id_list.json.gz: a list of released chemical reference
   entries, their content types (e.g., Chemical Component, BIRD), and
   the most recent modification date of the reference file.
 * released_structures_last_modified_dates.json.gz: a list of released
   PDB entries with the most recent modification date of the PDBx/mmCIF
   file.
 * unreleased_entries.json.gz: a list of on-hold PDB entries, their
   entry status, deposition date, and pre-release sequence information,
   where available.


Users are encouraged to utilize these inventory files. For example, 
checking for the update of the PDB archive can be performed using 
current_file_holdings.json.gz 
 or 
released_structures_last_modified_dates.json.gz 
 
in /pub/pdb/holdings/.


Please contact i...@wwpdb.org with any questions.

--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK



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