[ccp4bb] Register now for the triennial Ribosomes 2025 Conference at Asilomar June 22-27

[jp d]

Dear all,

Registration for Ribosomes 2025 is now open. 
This 19th triennial international ribosome conference will take place 
at the Asilomar Conference Ground in Pacific Grove, California, 
from June 22-27, 2025. 
The scientific program will feature talks and posters on the structure 
and function of ribosomes and the mechanisms of protein synthesis.

Registration and housing links are on the Ribosomes 2025 conference website

https://rna.ucsc.edu/rnacenter/ribosomes2025.  

We suggest that you register and book your lodging package as soon as possible 
since there is limited on-site housing at Asilomar. 
And please note that Abstracts must be submitted 
by April 1, 2025 in order to be considered for a talk.

If you have any questions, you can contact us at ribosomes2...@gmail.com.

(The Organizers)

Harry Noller

Laura Lancaster

Scott Blanchard

Kurt Fredrick



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Re: [ccp4bb] Diffraction data - Midwest Center for Structural Genomics (MCSG) structures

[Jose Artur Brito]

Dear All,

This bulletin is truly amazing, thank you for all the messages and 
replies!


I am already in contact with the people in charge of the project that 
superseded MCSG (Andrzej Joachimiak and Karolina Michalska).


Thank you also to Changsoo Chang that found the data and is about to 
send it to me!


Best regards,
Jose


---


On 17-03-2025 15:02, Jose Artur Brito wrote:

Dear All,
There are several structures deposited at the PDB which are authored
by the Midwest Center for Structural Genomics (MCSG).

I am interested in accessing the diffraction data for some of those
structures, namely a couple which have no associated publication.

Does anyone knows how to reach someone from the Center, namely Dr.
Andrzej Joachimiak which was the head of the project?

Thanks in advance, best regards,
Jose




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[ccp4bb] 7th International Symposium on Diffraction Structural Biology ( 5 - 7 May 2025)

[Kristina Djinovic Carugo]

Dear Colleagues,

We are delighted to announce the *Scientific Programme *for the *7th  
International Symposium on Diffraction Structural Biology (ISDSB2025) is 
now out! *The event will take place from *5–7 May 2025* at the *European 
Photon and Neutron Science (EPN) Campus in Grenoble, France,* at the 
European Photon and Neutron Science (EPN) Campus, Grenoble, France. It 
will be hosted by Partnership for Structural Biology (PSB) between 
European Molecular Biology Laboratory (EMBL), the European Synchrotron 
Radiation Facility (ESRF), the Institut Laue Langevin (ILL) and the 
Institut de Biologie Structurale (IBS).


The historical concept of the ISDSB Symposia is to bring together 
researchers using interactions of X-rays, electrons and neutrons with 
matter in the study of structural biology. Emphasis is also placed on 
integrating complementary approaches, such as studies of biological 
ultrastructure using microscopies and spectroscopies, including NMR, 
computational approaches. The symposia strive to maintain a balance 
between the development of cutting-edge methods and their application 
across relevant length scales, from molecular to cellular. Additionally, 
they serve as a platform to foster collaboration and exchange between 
academic and industrial researchers.


*Detailed Programme* is here:
https://www.psb-grenoble.eu/isdsb2025/

  Main session topics include:

  *     Studies of dynamic systems, 4D structural biology
  *     Electron and X-ray tomography, and correlative approaches
  *     Microcrystal Electron Diffraction of Proteins & small molecules
  *     Neutron Diffraction and Scattering for biological macromolecules
  *     From structure-based drug discovery to clinical trials
  *     Integrative approaches in Structural biology
  *     AI in structural biology, software and databases
  *     EPN research institutions and facilities

Registration deadline: *1 April 2025***
https://www.psb-grenoble.eu/isdsb2025

The IUCr Journals have endorsed our wish for a Collection of articles 
arising from the ISDSB 2025 be published in Acta Cryst D and Acta Cryst 
F, both from the lectures and the posters from those presenters that 
wish to do so. Guest Editors will be Kristina Djinovic Carugo, John R 
Helliwell and Atsushi Nakagawa.


There will be Poster sessions and also a Commercial and Industrial 
Companies Exhibition as well as a Visit to local Facilities.



On behalf of Local Organising Committee (LOC).

Kristina Djinović Carugo

LOC:
Florent Bernaudat, European Synchrotron Radiation Facility
Kristina Djinović Carugo, EMBL Grenoble
Frank Gabel, Insititut Laue Langevin
Andrew McCarthy, EMBL Grenoble
Antoine Royant, Institut de Biologie Structurale
Montserrat Soler Lopez, European Synchrotron Radiation Facility
--



-

*Kristina Djinovic Carugo*

Head of EMBL Grenoble

European Molecular Biology Laboratory (EMBL) Grenoble

71 Avenue des Martyrs

38000 Grenoble, France

Email:kristina.djino...@embl.org

Website: http://www.embl.fr

Tel:+33 4 76 20 7876; Secretary +33 4 76 20 7123

Mobile: +33 6 60 72 71 61

EMBL_logo



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Re: [ccp4bb] Diffraction data - Midwest Center for Structural Genomics (MCSG) structures

[Clemens Vonrhein]

Dear all,

at the bottom of

  https://staraniso.globalphasing.org/table1/

you'll find a (weekly updated) page that associates PDB entries with
(hopefully) raw diffraction data.

Cheers

Clemens


On Mon, Mar 17, 2025 at 03:02:33PM +, Jose Artur Brito wrote:
> Dear All,
> There are several structures deposited at the PDB which are authored by the
> Midwest Center for Structural Genomics (MCSG).
> 
> I am interested in accessing the diffraction data for some of those
> structures, namely a couple which have no associated publication.
> 
> Does anyone knows how to reach someone from the Center, namely Dr. Andrzej
> Joachimiak which was the head of the project?
> 
> Thanks in advance, best regards,
> Jose
> 
> 
> -- 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> 
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> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., 9 Journey Campus, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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Re: [ccp4bb] About generation of restraint file

[Tim Gruene]

On Tue, 18 Mar 2025 09:21:44 +0100
Christian Buratto  wrote:

> Dear CCP4 community,
> I am currently trying to determine the structure of a
> protein-polyoxometalate complex. I am using a polyoxometalate
> molecule that is a derivative of the one deposited in the CCDC (ICSD:
> 173439). I am facing difficulties in generating a restraint file for
> this metal-oxo molecule that can be recognized by Phenix, both for
> ReadySet and refinement jobs. I have attempted to use ACEdrg and
> ELBOW, but all my trials have been unsuccessful. A common error in
> refinement states that Phenix is unable to determine the energy type
> for Ru or W atoms present in my ligand molecule. If anyone has any
> suggestions or alternative approaches, I would greatly appreciate
> your input! Thank you all for your time and help.
> Best regards,
> Christian
> 
> 
> 
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Dear Christian,

sounds like a perfect task for the grade server,
https://grade.globalphasing.org
in combination of babel. Usually, I generate a PDB file (e.g. with
PLATON or SHELXL), then use babel to convert to mol2
obabel -o mol2 -O yourligand.mol2 yourligand.pdb

and upload the mol2-file to the grade server. This honours your atom
naming. Make sure the PDB input file includes a residue name (which is
easily done with SHELXL). 
Cheers,
Tim

-- 
--
Tim Gruene
Head of the Core Facility Crystal Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

https://ccsa.univie.ac.at

GPG Key ID = A46BEE1A



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Description: OpenPGP digital signature

Re: [ccp4bb] Dose-dependent evolution of the cryo-EM density of the disulfide bond (Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in Cryo-EM Structure

[Guillaume Gaullier]

Ah that's right, I had forgotten about this supplementary video. I even read 
this paper again not too long ago. It's working better than the HexAuFoil paper 
suggests it should, that's interesting to see. But it might not be generally 
applicable to all datasets? especially of lower resolution.


From: Tomas Malinauskas 
Sent: Monday, March 17, 2025 6:07:22 PM
To: Guillaume Gaullier
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Dose-dependent evolution of the cryo-EM density of the disulfide bond 
(Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in Cryo-EM 
Structure

Hi Guillaume,

Regarding your suggested experiment, something similar is presented in
Supplementary Video 2 in the following paper:
https://www.nature.com/articles/s41586-020-2829-0

Best wishes,
Tomas

On Mon, Mar 17, 2025 at 4:03 PM Guillaume Gaullier
 wrote:
>
> Hello,
>
>
> Sorry to hijack this discussion, but does someone know if reduction of a 
> disulphide could be a manifestation of radiation damage? Especially in 
> cryoEM, since we're shooting electrons at it.
>
>
> One way to test this would be to do a rough zero-dose extrapolation (repeat 
> motion correction with fewer and fewer frames, use the particle coordinates 
> and orientations determined with the full dose to extract particle images and 
> do reconstructions from the micrographs obtained with fewer frames) and see 
> if this feature appears with accumulated dose. But this is tricky to do if 
> motion correction is not perfect. At least according to the paper that 
> introduced HexAuFoil grids: https://doi.org/10.1126/science.abb7927 ; but I 
> don't know if anyone has tried even without these grids.
>
>
> Cheers,
>
>
> Guillaume
>
> 
> From: CCP4 bulletin board  on behalf of Artem 
> Evdokimov 
> Sent: Monday, March 17, 2025 4:50:37 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond 
> in Cryo-EM Structure
>
> To me this looks like a mixture of oxidized and reduced states of the S-S 
> bond. Hard to say with any certainty seeing as the (optical) resolution is 
> modest.
>
> Artem
>
> - Cosmic Cats approve of this message
>
>
> On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar  wrote:
>>
>> Hello Everyone,
>>
>> I am worried about the density of the disulfide bond in the cryo-EM 
>> structure that I am analyzing. The experimental map shows the expected 
>> density for the disulfide bond involving two cysteine residues, but in 
>> addition, I see some unexplained density, which I do not know how to 
>> interpret.
>>
>> I have attached the figure for your reference. Does anyone have experience 
>> with such extra density around a disulfide bond in their structures? Any 
>> thoughts would be greatly appreciated.
>>
>> Thanks for your attention and assistance.
>>
>> Warm regards
>> Devbrat kumar
>> Postdoctoral Fellow
>> IITD, In
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>
> 
>
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>
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>
>
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>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär det 
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Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in Cryo-EM Structure

[Guillaume Gaullier]

Thank you Wim, this is an interesting read. Do you also have a reference about 
radiation damage in electron microscopy?


From: CCP4 bulletin board  on behalf of Wim Burmeister 

Sent: Monday, March 17, 2025 5:27:21 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in 
Cryo-EM Structure


Hello,

go back to the basics:


Burmeister, W. P.

Structural changes in cryo-cooled protein crystals owed to radiation damage.

Acta Cryst. D 56, 328-341 (2000). https://doi.org/10.1107/S0907444999016261


Wim



On 17/03/2025 17:03, Guillaume Gaullier wrote:

Hello,


Sorry to hijack this discussion, but does someone know if reduction of a 
disulphide could be a manifestation of radiation damage? Especially in cryoEM, 
since we're shooting electrons at it.


One way to test this would be to do a rough zero-dose extrapolation (repeat 
motion correction with fewer and fewer frames, use the particle coordinates and 
orientations determined with the full dose to extract particle images and do 
reconstructions from the micrographs obtained with fewer frames) and see if 
this feature appears with accumulated dose. But this is tricky to do if motion 
correction is not perfect. At least according to the paper that introduced 
HexAuFoil grids: https://doi.org/10.1126/science.abb7927 ; but I don't know if 
anyone has tried even without these grids.


Cheers,


Guillaume


From: CCP4 bulletin board  
on behalf of Artem Evdokimov 

Sent: Monday, March 17, 2025 4:50:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in 
Cryo-EM Structure

To me this looks like a mixture of oxidized and reduced states of the S-S bond. 
Hard to say with any certainty seeing as the (optical) resolution is modest.

Artem

- Cosmic Cats approve of this message


On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar 
mailto:devformed...@gmail.com>> wrote:
Hello Everyone,

I am worried about the density of the disulfide bond in the cryo-EM structure 
that I am analyzing. The experimental map shows the expected density for the 
disulfide bond involving two cysteine residues, but in addition, I see some 
unexplained density, which I do not know how to interpret.

I have attached the figure for your reference. Does anyone have experience with 
such extra density around a disulfide bond in their structures? Any thoughts 
would be greatly appreciated.

Thanks for your attention and assistance.

Warm regards
Devbrat kumar
Postdoctoral Fellow
IITD, In



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--

Wim Burmeister
Professor
Institut de Biologie Structurale (IBS) CIBB
71 avenue des Martyrs / CS 20192
38044 Grenoble Cedex 9, FRANCE
E-mail: wim.burmeis...@ibs.fr
Mobile:   +33 (0) 7 50 49 19 91
website



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[ccp4bb] About generation of restraint file

[Christian Buratto]

Dear CCP4 community,
I am currently trying to determine the structure of a
protein-polyoxometalate complex. I am using a polyoxometalate molecule that
is a derivative of the one deposited in the CCDC (ICSD: 173439).
I am facing difficulties in generating a restraint file for this metal-oxo
molecule that can be recognized by Phenix, both for ReadySet and refinement
jobs. I have attempted to use ACEdrg and ELBOW, but all my trials have been
unsuccessful. A common error in refinement states that Phenix is unable to
determine the energy type for Ru or W atoms present in my ligand molecule.
If anyone has any suggestions or alternative approaches, I would greatly
appreciate your input!
Thank you all for your time and help.
Best regards,
Christian



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[ccp4bb] Spreadsheet DoE for optimising protein production & characterisation

[Stollar, Elliott]

Hi all,

Please find here: https://zenodo.org/records/13998442 a series of factorial 
design spreadsheets we developed to help your lab optimise protein expression, 
purification, crystallisation, stability etc. These are free to download and 
are intended to lower the barrier/cost for using this powerful approach in the 
lab.


Thanks and Best wishes,

Elliott Stollar

Click for contact info



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[ccp4bb] Change e-mail address

[Doriano Lamba]

Hi,

I am kindly enquiring whether it would be possible to change the email to which 
my ccp4i bulletin board emails get sent.

Old e-mail address: doriano.la...@ic.cnr.it

New email address: doriano.la...@cnr.it

Thank you very much!

Doriano Lamba



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[ccp4bb] Reminder: CBMS Lecture Series - March 19, 13:30 (EST) - Bowman

[Stojanoff, Vivian]

You are cordially invited to join the Center for Biomolecular Structure Lecture 
Series …


SARAH E. J. BOWMAN


University at Buffalo
Jacobs School of Medicine and Biomedical Sciences

WEDNESDAY, MARCH 19, 13:30 (EST)


"Shining light on metalloproteins: Multiple methods tell the story"

Register in advance for this meeting:

https://bnl.zoomgov.com/meeting/register/vJIsduuoqDgjG0VGQ_c-iX5BQbFo4OQunpU

  Time conversion Link: 
https://www.worldtimebuddy.com/

Abstract: Diffraction-based structural biology methods are a fundamental tool 
for structural science, accounting for close to 85% of all macromolecular 
structures deposited to the Protein Data Bank. Recent advances in structural 
biology methods, from synchrotron, electron diffraction, and XFELs to 
computational advances and CryoEM, have opened the door to the investigation of 
more challenging target samples. This talk will highlight several research 
projects in the Bowman Lab on metalloprotein biology and the methods available 
to discover how structure contributes to their unique chemistry. Metals in 
proteins are ubiquitous (involving up to 50% of the proteome) and involved in 
many of the reactions that define life – transfer of energy, photosynthesis, 
metabolism, oxygen shuttling, and much more. In structural work, X-ray and 
electron sources used in diffraction and CryoEM studies can cause changes in 
oxidation state and radiation damage, obscuring the true nature of the role of 
the metal in the protein. We are working to make use of multiple methods, 
including spectroscopy coupled to diffraction data collection and specialized 
fixed-target platforms, to probe metalloprotein biology. This suite of 
approaches facilitates examination of protein structure and opens paths to 
further studies of protein dynamics and motion.

=
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e lifescie...@bnl.gov
w https://www.bnl.gov/ps/lifesciences/

Address:
Center for Biomolecular Structure
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973






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