[ccp4bb] EMBO workshop on Molecular Neurobiology deadline April 5th
Dear colleagues, I would like to bring your attention to a workshop <https://meetings.embo.org/event/22-mol-neurobio> that will take place from May 23rd-27th 2022 near Heraklion in Crete Greece that brings together structural biologists, microscopists and neurobiologists interested in mechanisms involved in neuronal organization. The meeting is organized by Elena Seiradake from Oxford University, and co-organized by Marc Tessier-Lavigne (Stanford) Alex Kolodkin (John Hopkins), Naoko Mizuno (NIH), Valentin Nagerl (Bordeaux) and Amparo Acker-Palmer (Goethe University) and takes place in an all-inclusive hotel at the seaside. A spectacular venue with a spectacular cast! The registration deadline is 5th of April 2022. Please consider joining us: https://meetings.embo.org/event/22-mol-neurobio Best wishes, Rob -- Rob Meijers, PhD Interim Executive Director Director of the Antibody Platform Institute for Protein Innovation 4 Blackfan Circle, Room 921A Boston, MA 02115-5713, USA phone: +1 617-651-8328 email: rob.meij...@proteininnovation.org LinkedIn <https://www.linkedin.com/company/proteininnovation/> • Instagram <https://www.instagram.com/ipi_protein/?hl=en> • Twitter <https://twitter.com/IPI_Protein> [image: A close up of a sign Description automatically generated] <https://proteininnovation.org/> -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] (Senior) scientist Antigen Production at the Institute for Protein Innovation in Boston, USA
Dear colleagues, the Institute for Protein Innovation (IPI) is developing human synthetic IgG antibodies for the human cell surfaceome, with a special emphasis on cell surface receptors involved in neuronal development, immunotherapy and cancer. We are looking for a structural biologist with experience in the design, production and structural characterization of cell surface receptors to strengthen our antigen production team. For more information about the job and the institute, see here: https://proteininnovation.org/job-listings/2021/1/25/scientist-or-senior-scientist-antigen-production and feel free to contact me directly. Applications should be sent to care...@proteininnovation.org Best regards, Rob Meijers Head of Biological Discovery Institute for Protein Innovation -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] EMBL Postdoc position available in structural neurobiology
Dear all, a three year postdoctoral position is available within the EIPOD (EMBL Interdisciplinary Postdocs) scheme in my group to study the role of the netrin receptor UNC5B in neuronal cell death. A more detailed description can be found here: http://www.embl.de/training/postdocs/08-eipod/application/04_2014_project_ideas/meijers.pdf The research will take place at the EMBL Hamburg Outstation in Germany, in collaboration with the group of Francesca Peri at EMBL Heidelberg. Candidates with a background in protein crystallography and affinity with cell biology are encouraged to apply. For more information on the EIPOD scheme, please visit: http://www.embl.de/training/postdocs/08-eipod/index.html A successful application will require a written motivation as to why this project is suitable, and candidates are therefore encouraged to contact me directly. The deadline for the application is 11th of September 2014. Best regards, Rob Meijers Group Leader EMBL Hamburg http://www.embl-hamburg.de/research/unit/meijers/contact/index.html
[ccp4bb] Deadline approaching: EMBO course on protein expression, purification and crystallization
Dear all, this is a reminder that the deadline for application to the EMBO Practical Course Protein expression, purification and characterization/crystallization (PEPC9) is 18th of May. The course will be held at EMBL Hamburg from the 8th of September until the 16th of September 2014. This is an extensive hands-on course with practicals in cloning, expression (E. coli Baculo virus), purification (with and without tags) and characterization (CD, thermofluor, light scattering and crystallization). The course is aimed at PhD students and postdoctoral students who want to improve their protein production skills to be able to structurally characterize their proteins. Tutors include: Imre Berger, EMBL Grenoble (MultiBac system) Huseyin Besir, EMBL Heidelberg (Cloning) Louise Bird, OPPF, Oxford University (E. coli expression) Opher Gileadi, SGC, Oxford University (Purification optimization) Martin Halberg, Karolinksa Institutet (Thermofluor and other optimization techniques) Michael Marr, Brandeis University (CSH course on protein purification) David Hacker, EPFL Lausanne (Mammalian cell expression) Alex McPherson, University of California (protein crystallization) Preben Morth, University of Oslo (membrane protein production crystallization) Joanne Nettleship, University of Oxford (E. coli expression) Janet Newman, CSIRO (Crystal optimization) Dmitri Svergun, EMBL Hamburg (SAXS) Participants are encouraged to bring their own sample to the course for cloning and expression in E. coli and baculo-virus, high-throughput crystallization, and biophysical characterization. A more extensive characterization of samples is possible under the auspices of Biostruct-X: http://www.biostruct-x.eu/content/apply-funding For more information, please visit our website: http://events.embo.org/14-pepc/ or contact us by email: pe...@t-online.de Best regards, Rob Meijers, , Annabel Parret, Stephane Boivin Christian Loew EMBL Hamburg Notkestrasse 85 D-22603, Hamburg, Germany
[ccp4bb] Announcement: EMBO Practical Course on Protein Expression, Purification and Characterization (PEPC9)
Dear all, we are pleased to announce that applications are open for the EMBO Practical Course Protein expression, purification and characterization/crystallization (PEPC9), which will be held at EMBL Hamburg from the 8th of September until the 16th of September 2014. This is an extensive hands-on course with practicals in cloning, expression (E. coli Baculo virus), purification (with and without tags) and characterization (CD, thermofluor, light scattering and crystallization). The course is aimed at PhD students and postdoctoral students who want to improve their protein production skills to be able to structurally characterize their proteins. Speakers include: Imre Berger, EMBL Grenoble (MultiBac system) Huseyin Besir, EMBL Heidelberg (Cloning) Louise Bird, OPPF, Oxford University (E. coli expression) Opher Gileadi, SGC, Oxford University (Purification optimization) Martin Halberg, Karolinksa Institutet (Thermofluor and other optimization techniques) Michael Marr, Brandeis University (CSH course on protein purification) David Hacker, EPFL Lausanne (Mammalian cell expression) Alex McPherson, University of California (protein crystallization) Preben Morth, University of Oslo (membrane protein production crystallization) Joanne Nettleship, University of Oxford (E. coli expression) Janet Newman, CSIRO (Crystal optimization) Dmitri Svergun, EMBL Hamburg (SAXS) Participants are encouraged to bring their own sample to the course for cloning and expression in E. coli and baculo-virus, high-throughput crystallization, and biophysical characterization. A more extensive characterization of samples is possible under the auspices of Biostruct-X: http://www.biostruct-x.eu/content/apply-funding For more information, please visit our website: http://events.embo.org/14-pepc/ or contact us by email: pe...@t-online.de Best regards, Rob Meijers, , Annabel Parret, Stephane Boivin Christian Loew EMBL Hamburg Notkestrasse 85 D-22603, Hamburg, Germany
[ccp4bb] Sponsored) access to the integrated facility for structural biology at EMBL Hamburg
Dear all, the integrated facility at EMBL Hamburg at the PETRA3 synchrotron in Germany consists of two macromolecular crystallography beamlines, a BioSAXS beamline and a laboratory for sample preparation and characterization. For those of you who are interested in a comprehensive characterization of their sample, it might be worth to consider to extend your synchrotron visit and include additional experiments. The integrated facility includes: - Offline protein purification and characterization by circular dichroism, dynamic and static light scattering (can be booked with beamtime) - Online gel filtration and light scattering at the BioSAXS beamline - A high-throughput crystallization facility Samples can be shipped, and experiments can be monitored remotely through a dedicated web interface - Crystal screening on the crystallography beamlines - Quality control protocols All incoming samples for crystallization are tested by mass spectrometry and thermal shift assay, and a report is returned to the user - Sample optimization - Inhouse thermofluor screens to optimize purification, conditioning and crystallizability - Limited proteolysis - Expert staff that assists in the planning, execution and analysis of experiments Access to these facilities is funded by the European Union under the FP7 Biostruct-X grant. For more information on gaining sponsored access please visit: http://www.biostruct-x.eu/content/apply-funding For more information on the facilities, please visit: http://www.embl-hamburg.de/facilities/index.html or send an email to s...@embl-hamburg.de Best regards, Rob Meijers Group Leader EMBL Hamburg Outstation P: +49 40 89902 243 EMBL c/o DESY F: +49 40 89902 149 Notkestrasse 85 D-22603 Hamburg, Germany
[ccp4bb] Reminder: Deadline 20th of May for application to the PEPC8 EMBO Practical course
Dear all, this is a reminder that the deadline for application to the EMBO Practical Course Protein expression, purification and characterization (PEPC8) is on Sunday the 20th of May. The course will be held at EMBL Hamburg from the 3rd of September until the 11th of September 2012. This is a hands-on course with practicals in cloning, expression (E. coli Baculo virus), purification (with and without tags) and characterization (thermofluor, circular dichroism, SAXS, crystallization and in-situ dynamic light scattering, ITC and thermophoresis). Speakers include: Imre Berger, EMBL Grenoble Huseyin Besir, EMBL Heidelberg Christian Betzel, University of Hamburg Louise Bird, Oxford University Uwe Bierfreund, GE Healthcare Richard Burgess, University of Wisconsin-Madison Stefan Duhr, NanoTemper David Hacker, EPFL Lausanne Josan Marquez, EMBL Grenoble Alex McPherson, University of California Preben Morth, University of Oslo Jochen Mueller-Dieckmann, EMBL Hamburg Joanne Nettleship, University of Oxford Ilme Schlichting, Max Planck Institute, Munich Dmitri Svergun, EMBL Hamburg Participants are encouraged to bring their own sample to the course for cloning and expression in the pOPIN vectors, crystallization, SAXS and biophysical characterization. A more extensive characterization of samples is sponsored in context of the course by the co-sponsor Pcube. For more information, please visit our website: http://events.embo.org/12-pepc/index.html or contact us by email: pep...@googlemail.com Best regards, Rob Meijers, Stephane Boivin, Annabel Parret Dmitri Svergun EMBL Hamburg Notkestrasse 85 D-22603, Hamburg, Germany
[ccp4bb] Announcement: EMBO Practical Course in protein expression, purification and characterization (PEPC8)
Dear all, we are pleased to announce that applications are open for the EMBO Practical Course Protein expression, purification and characterization (PEPC8), which will be held at EMBL Hamburg from the 3rd of September until the 11th of September 2012. This is a hands-on course with practicals in cloning, expression (E. coli Baculo virus), purification (with and without tags) and characterization (thermofluor, SAXS, crystallization and in-situ dynamic light scattering, ITC and thermophoresis). Speakers include: Imre Berger, EMBL Grenoble Huseyin Besir, EMBL Heidelberg Christian Betzel, University of Hamburg Louise Bird, Oxford University Uwe Bierfreund, GE Healthcare Richard Burgess, University of Wisconsin-Madison Stefan Duhr, NanoTemper David Hacker, EPFL Lausanne Josan Marquez, EMBL Grenoble Alex McPherson, University of California Preben Morth, University of Oslo Jochen Mueller-Dieckmann, EMBL Hamburg Joanne Nettleship, University of Oxford Ilme Schlichting, Max Planck Institute, Munich Dmitri Svergun, EMBL Hamburg Participants are encouraged to bring their own sample to the course for cloning and expression in the pOPIN vectors, high-throughput crystallization, SAXS and biophysical characterization. A more extensive characterization of samples is sponsored in context of the course by the co-sponsor Pcube. For more information, please visit our website: http://events.embo.org/12-pepc/index.html or contact us by email: pep...@googlemail.com Best regards, Rob Meijers, Stephane Boivin, Annabel Parret Dmitri Svergun EMBL Hamburg Notkestrasse 85 D-22603, Hamburg, Germany
Re: [ccp4bb] Unexplained density near cobalt
Are the imidazole rings of the histidines distorted? If they are, it could be water/hydroxide. If not, it is probably a cobalt ion side show. Cheers, Rob Meijers EMBL Hamburg --- On Thu, 7/7/11, Artem Evdokimov artem.evdoki...@gmail.com wrote: From: Artem Evdokimov artem.evdoki...@gmail.com Subject: Re: [ccp4bb] Unexplained density near cobalt To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, July 7, 2011, 9:39 PM Could be a hexacoordinated cobalt with a water molecule (or a hydroxyl ion) depending on the chemical environment... Artem On Thu, Jul 7, 2011 at 10:07 AM, Machius, Mischa Christian mach...@med.unc.edu wrote: Y'all, I was wondering if anyone had any thoughts about a feature we observe with a metal-binding site: we have a cobalt that is bound by four histidines and one carboxyl group. There is extra density near the cobalt. See pictures below. The extra density spans the NE2 atoms from two histidines. The Fo-Fc peak (green) has a height of up to 10 sigma (eight molecules in the asymmetric unit, all showing the same feature). I placed a water molecule into the density to get some distances: the distances between the peak and the neighboring histidine NE2 atoms is ~1.8Å and ~2.0Å, resp. The distance between the peak and the cobalt is ~1.7Å. The resolution is 1.24Å. Any input would be greatly appreciated. Many thanks in advance! Cheers! MM
[ccp4bb] Postdoctoral position in structural neuroscience
Dear all,
on behalf of Jia-huai Wang, I post this message. For inquiries please contact
Jia-huai at jw...@dfci.harvard.edu.
Rob Meijers
p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size:
12pt; font-family: Times New Roman; }div.Section1 { page: Section1; }
Postdoctoral fellow position in structural neuroscience
The successful candidate will focus his/her research on the
elucidation of molecular mechanisms with which neuro-receptors play part in
neuronal development and the immune function in the central nervous system
(CNS). These include their functions in axon guidance and neuron-glia
interaction that mediates key immunological protection for the CNS. The project
is a close collaborative effort between Professor Wang's structural biology lab
and Professor Zhang's neuroscience lab.
The position requires a PhD. degree with a strong background
in molecular biology and protein chemistry. Experience in crystallography
and/or neuroscience will be a plus, but not absolutely required. Highly
motivated individuals are encouraged to apply. The position will essentially be
based at Peking University in Beijing, China, with the opportunity of doing
some research at Harvard Medical School in Boston.
Interested candidates please email a cover letter, CV, 3
reference names, as well as an email address and telephone number to Drs.
Jia-huai Wang or Yan Zhang at jw...@red.dfci.harvard.edu and
yanzh...@pku.edu.cn.
Re: [ccp4bb] nad woes
Hi Jan, at low occupancy (and I suppose a resolution that does not extend beyond 2.0 A), you have to rely on your restraints. I think the consensus is that the adenine ring should be planar. The pyridine ring of the nicotinamide should be flat if the ring is oxidized (NAD+), and can be distorted when reduced (NADH). Most NAD molecules in the PDB have strict planar restaints in the pyridine ring of the nicotinamide, even when the density clearly shows that they are puckered. Many NAD+ cofactors get converted to NADH during crystallization by the enzyme they bind. Especially PEG can contain a substrates to convert NAD+ into NADH in the crystal. Best regards, Rob Meijers Synchrotron Soleil --- On Thu, 3/19/09, Jan Abendroth jan.abendr...@gmail.com wrote: From: Jan Abendroth jan.abendr...@gmail.com Subject: [ccp4bb] nad woes To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, March 19, 2009, 12:50 AM Hi all, is there any wisdom on NAD out there? I experience some strange behaviour of this common cofactor. With moderately convincing density, probably low occupancy of a cofactor that came along for the ride from E coli, Refmac5.5.0088 pulls the AN6 atom out of the adenine plane. With my own library that puts planar restraints on the adenine ring this seems to be fixed. Coot during real space refinement or regularisation using either the standard or my own dictionary handles the purine ring just fine, however, totally garbles up the nicotineamide. Btw, I use the * nomenclature. Cheers Jan -- Jan Abendroth deCODE biostructures Seattle / Bainbridge Island WA, USA work: JAbendroth_at_decode.is home: Jan.Abendroth_at_gmail.com
[ccp4bb] Deadline EMBO Practical Course on X-ray crystal structure determination of macromolecules
Dear Community, this is a gentle reminder that the deadline for applications (15th of May) is approaching for the EMBO Practical Course X-ray crystal structure determination of macromolecules at the Synchrotron Soleil from 14 - 21 September 2008 This course is meant as an introduction to the determination of protein/DNA X-ray structures, and covers the process from construct design till validation deposition of the structure in the PDB. Lectures will be combined with practicals on the PROXIMA I beamline, on crystallization, SAD/MAD structure determination, structure refinement, model building and validation. Students are encouraged to bring their own samples. Tutors include: Kevin Cowtan, Anastassis Perrakis, Jim Pflugrath, Randy Read, Jane Richardson, Thomas Schneider, Bill Shepard, Enrico Stura, Piotr Sliz, Andy Thompson, Herman van Tilbeurgh, Clemens Vonrhein and Peter Zwart. Course registration and accommodation/meals are free for academic participants. There are four travel grants available for students from Croatia, Czech Republic, Estonia, Greece, Hungary, Israel, Poland, Portugal, Slovakia, Slovenia and Turkey. For more information and participant registration, please visit the course website at: http://cwp.embo.org/pc08-26/ Regards, Rob Meijers Synchrotron Soleil - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
Re: [ccp4bb] Low resol structure
Dear Jim, I guess you entered the ABC transporter zone. You say you use the structure to show the movement of helices. One important point is whether this structure is based on a molecular replacement solution, or it was built from experimental phases. There are numerous cases where adding some experimental phasing helped to convince the editors. Good luck, Rob Meijers Synchrotron Soleil Jim Naismith [EMAIL PROTECTED] wrote: Dear All, I have an interesting problem, we have a 3.45A structure of a membrane protein. We have just been told that the structure is too low resolution to be considered as the uncertainty is too high. We use the structure to identify helices which have moved. Is there a blanket ban on low res structure operating at the moment? The structure was refined extremely tightly, MolPROB 98th centile. (I will happily send the data and structure to anyone who wishes to validate.) The editors simply ignored everything but the res limit (I/sI in the last shell was 1.8 with a redundancy of 4) Of course we will begin the usual journal shopping. However, does anyone know how to convince editors and non-xtallographers that 3.45A is valid? Best Jim James H. Naismith FRSE |Research mailto:[EMAIL PROTECTED] Professor of Chemical Biology|Teaching mailto:[EMAIL PROTECTED] Centre for Biomolecular Sciences |Office: 1334-463792 The North Haugh |Fax : 1334-467229 The University |Lab : 1334-467245 St. Andrews |In UK add 0 to start of number Fife Scotland, U.K., KY16 9ST|http://www.st-and.ac.uk/~strucbio The University of St Andrews is a charity registered in Scotland : No SC013532 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
[ccp4bb] Announcement: EMBO Practical course on X-ray crystal structure determination
Dear community,Dear community, This is an announcement for a EMBO/MAX-INF2 practical course X-ray crystal structure determination of macromolecules to be held at the Soleil Synchrotron near Paris (France), from the 14th-21st of September 2008. This course is meant as an introduction to the determination of protein/DNA X-ray structures, and covers the process from construct design till validation deposition of the structure in the PDB. Lectures will be combined with practicals on crystallization, SAD/MAD structure determination, structure refinement, model building and validation. Tutors include: Kevin Cowtan, Anastassis Perrakis, Jim Pflugrath, Randy Read, Jane Richardson, Thomas Schneider, Bill Shepard, Enrico Stura, Piotr Sliz, Andy Thompson, Herman van Tilbeurgh, Clemens Vonrhein and Peter Zwart. Course registration and accommodation/meals are free for academic participants. There are four travel grants available for students from Croatia, Czech Republic, Estonia, Greece, Hungary, Israel, Poland, Portugal, Slovakia, Slovenia and Turkey. For more information and participant registration, please visit the course website at: http://cwp.embo.org/pc08-26 Best regards, Rob Meijers Beamline Scientist PROXIMA II Synchrotron Soleil - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
Re: [ccp4bb] Removal of glycosylation sites in Picha expression construct
Dear Evette, it is quite common that mutation of glycosylation sites completely kills expression. One rationale is that the glycans cover hydrophobic patches on the surface of the protein, and when exposed, the protein won't fold properly anymore. Pichia is a pain because the glycans it produces are enormous and heterogenous. That means that when you deglycosylate, you end up with a protein sample that has glycans of varying length which certainly does not help in crystallization. There are some commercial pichia strains out there with a modified glycosylation machinery. But I would certainly commend Artem's suggestion to switch to baculo. Cheers, Rob Meijers Synchrotron Soleil Radisky, Evette S., Ph.D. [EMAIL PROTECTED] wrote: Removal of glycosylation sites in Picha expression construct Dear all, Our lab is new to working with Pichia pastoris, also new to working with glycosylated proteins. We have a construct for a secreted protein that expresses pretty well in Picha, but upon mutation of the 2 N-linked glycosylation sites to Ala, we get no expression at all, nada. The nucleic acid sequence appears to be correct, i.e. we have not introduced any unintentional frame shifts, stop codons, or anything like that. Is this a common phenomenon? Are there any tricks to get the Pichia to do its thing? Any chance that alternative substitutions will work when Ala does not? Or are we better off (a) trying to deglycosylate enzymatically, or (b) trying a different expression host? All opinions and anecdotes welcome. Thanks! Evette Evette S. Radisky, Ph.D. Assistant Professor and Associate Consultant II Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372 (office) (904) 953-0046 (lab) - Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.
