[ccp4bb] Postdoc position for noncoding RNAs-protein complexes

[Nakanishi, Kotaro]

The Nakanishi lab at The Ohio State University 
(https://u.osu.edu/nakanishilab/) is looking for a highly motivated and skilled 
postdoc.  Our group aims to understand how noncoding RNAs work with their 
cognate proteins to regulate gene expression.  We study human macromolecules 
involved in critical cellular events in normal conditions and diseases.  The 
successful candidates must have a Ph.D. and expertise in X-ray crystallography. 
 Practical skills (protein production on a large scale, protein purification 
using FPLC, crystallization, data collection, and structure determination) are 
essential.  Experience in Cryo-EM is advantageous.  For more information, 
please visit our website.

The position is available immediately.  The annual salary wage is $48,000 - 
60,000 for three years (renewable).  The weather in Columbus is stable, and the 
living cost is reasonable.  So, postdocs can focus on their research to build a 
successful career.

Interested candidates should send the following directly to nakanish...@osu.edu.
• CV including a publication list.
• One-page research statement including 1. the current work, 2. the reason for 
joining our
group, and 3. the future goals after postdoc training.
• Contact information of three references.



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[ccp4bb] 2023 ACA Meeting - Abstracts due March 24

[Sarah Bowman]

Hi everyone,

The Annual ACA Meeting will be in Baltimore, MD from July 7 - July 11, 2023!  
Program details here.

Abstract submission deadline is 
March 24, 2023!

Biological Macromolecules SIG is sponsoring & co-sponsoring a great lineup of 
sessions – check out the list below!

Saturday 7/8/2023
1.1.5: Crystal Growth (Co-chairs: Gabby Budziszewski, Xu Liu)
1.2.2: Complementary methods to study metalloenzymes (Co-chairs: Gloria 
Borgstahl, Nicholas Schnicker)

Sunday 7/9/2023
2.1.2: Structures from Artificial Intelligence (Co-chairs: Jennifer Wierman, 
Melanie Vollmar)
2.1.5: DEI: expanding access & opportunities in structural science (Co-chairs: 
Eta Isiorho, Christina Bourne)
2.2.5: Serial Crystallography (Co-chairs: Iris Young, Petra Fromme)
2.2.6: Enzyme allostery (Co-chairs: Will Thomas, Max Watkins)
2.3.1: Career Odysseys (Co-chairs: Samantha Powell, Daniel Kneller)

Monday 7/10/2023
3.1.3: Updates from structural genomics (Co-chairs: David Rose, Stephen Burley)
3.1.5: New Sample preparation technology for cryo-EM and cryo-ET (Co-chairs: 
Jianhua Zhao, David Taylor)
3.2.5: Hot Structures (Co-chairs: Charles Stewart, Jonathan Clinger)
3.2.6: Structure of nucleic acid (Co-chairs: Melanie Ohi, Yuan He)
3.3.1: Would You Publish This? (Co-chairs: Matthew Brown, Rebecca McAuliffe)

Tuesday 7/11/2023
4.1.3: Structure Based Drug Design (Chair: Elizabeth Sprague)
4.1.4: One Weird Trick (Co-chairs: Charles Bou-Nader, Jonathan Hermann)
4.2.4: Electron Tomography (Co-chairs: Lindsey Backman, Devrim Acehan)
4.2.5: Microcrystal Electron Diffraction of Proteins (MicroED) (Co-chairs: 
Sarah Bowman, Brent Nannenga)

Cheers,
Sarah

Sarah EJ Bowman PhD
Associate Investigator | Hauptman-Woodward Medical Research Institute
Director | National High-Throughput Crystallization Center
Research Associate Professor | Department of Biochemistry | University at 
Buffalo

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Research Webpage
Crystallization Center Webpage

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203



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Re: [ccp4bb] NMR structires

[mesters@biochem]

Maybe intensional to stress the word „paradoxal“ included in the title of the 
deposition? Same could be true for the related entry 1HIS to stress the word 
„dynamics“?

I guess back in in 1993-1994, structures were not checked rigorously…

Jeroen
--
Dr. math. et dis. nat. Jeroen R. Mesters
https://orcid.org/-0001-8532-6699
University of Lübeck
Institute of Biochemistry
https://www.biochem.uni-luebeck.de
phone: +49-451-3101-3105
Ratzeburger Allee 160
23562 Lübeck
Germany
--

> Am 02.03.2023 um 16:09 schrieb Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
> 
> I have been looking at 1hiq - an NMR structure with 20 models.
> I had always assumed that an attempt had been made to overlap the first with 
> the second, third etc, but this does not seem to be so for this structure..
> Have I been labouring under a misapprehension?
> Eleanor Dodson
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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[ccp4bb] NMR structires

[Eleanor Dodson]

I have been looking at 1hiq - an NMR structure with 20 models.
I had always assumed that an attempt had been made to overlap the first
with the second, third etc, but this does not seem to be so for this
structure..
Have I been labouring under a misapprehension?
Eleanor Dodson



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[ccp4bb] Looking for a post-doc with solid knowledge in cryo-EM

[Marc Graille]

The Graille lab is interested in understanding how epitranscritomic marks are 
deposited on RNAs and influence RNA translation and decay as well as cell 
proliferation and organ development. We currently use a combination of various 
experimental approaches : molecular biology, biochemistry, cell biology and 
structural biology. We are willing to develop cryo-EM studies on human 
ribosomes as well as on complexes between RNA modifying enzymes and their 
substrates. The lab has access to an in-house cryo-EM platform equipped with a 
LEICA EM-GP sampler plunger to prepare grids and a Titan THEMIS cryo-electron 
microscope (200 kV). Access to Titan KRIOS machines is possible on French or 
European facilities.

This project will be realized at the Laboratory of Structural Biology of the 
Cell (BIOC) from Ecole Polytechnique (Institut Polytechnique de Paris - IPP; 
Palaiseau; France), a leading French institute that combines top-level 
research, academics, and innovation at the cutting-edge of science and 
technology. The laboratory is located 40 minutes by train from Paris City 
centre. The campus offers all the equipments to perform various activities 
(music, theater…) or sports: swimming pools, 8 tennis courts, several football, 
badminton, tennis table, volleyball and basketball pitches, climbing walls, …

The lab is looking for a candidate with solid knowledge in cryo-EM. The 
successful candidate will work in close collaboration with the team of Dr 
Schmitt and Mechulam, who have developed a strong expertise in cryo-EM since 
more than ten years. The selected candidate will apply to various local 
(Institut Polytechnique de Paris), national (charities such as FRM) or 
international (EMBO, Marie Curie, …) calls to get a post-doctoral fellowships 
to join the lab. The applicants should be preparing or hold a PhD degree with 
demonstrated knowledge in cryo-EM analysis of macromolecular complexes. Planned 
start date : Spring 2024.

Working knowledge of the English language (scientific, oral and written) is 
necessary, but knowledge of French is not required as the team regularly hosts 
people from different countries. Enthusiasm, motivation and willingness to 
contribute to a dynamic and enjoyable working environment are very important 
qualities. The candidate should show autonomy, but a successful integration 
into the team projects is essential.

Applications (including a detailed CV, summary of your current project and 
relevant skills and a contact information of two/three references) or 
information requests should be sent to Marc Graille 
(marc.grai...@polytechnique.edu).
Website: http://bioc.polytechnique.fr/spip.php?rubrique117=en 

Twitter : @GrailleLab

—
Marc GRAILLE, PhD
DR1-CNRS
Laboratoire de Biologie Structurale de la Cellule  (BIOC; Ex-Laboratoire de 
Biochimie)
UMR7654 du CNRS

Head of the team: “Translation and degradation of eukaryotic mRNAs”

ÉCOLE POLYTECHNIQUE 
91128 PALAISEAU CEDEX
FRANCE 
: +33 (0)1 69 33 48 90


 : marc.grai...@polytechnique.edu  / 
Twitter : @GrailleLab 
https://portail.polytechnique.edu/bioc/en/research/coupling-between-translation-and-mrna-degradation-eukaryotes
—






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Re: [ccp4bb] Tools for structure-based multiple sequence alignment

[Harry Powell]

Hi Manoj

If the structures are in the PDB, then PDB-KB may have already done the work 
for you - 

https://www.ebi.ac.uk/pdbe/pdbe-kb/

They run Gesamt on homologous structures for the whole PDB every week (as I 
understand it).

Harry

> On 2 Mar 2023, at 07:45, Manoj N  wrote:
> 
> Dear all,
> We want to generate a structure-based multiple sequence 
> alignment for a large number of homologous structures (>100). 
> 
> What are the available programs (stand-alone or webserver) to do this? 
> 
> Thank you,
> Best wishes,
> Manoj
> 
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> 



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