SBGrid Consortium - News and Events

Newsletter for September 2021

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Published September 2021

Dear Consortium Members and Affiliates,

School is back in session and we are fortunate here in Boston that the streets are not as eerily quiet as they were this time last year. Our news this month: webinars have resumed, we have a profile on SBGrid member Gabby Rudenko, a software push with 4 updates and one new title, 8 new members to welcome, a new auto-update feature in our software installation manager, a CryoEM focused webinar mini-series for the Australasian community, and 3 member publication highlights.

CONGRATULATIONS! to SBGrid members Sun Hur of Harvard Medical School, Vanessa Ruta of The Rockefeller University, Vincent Tagliabracci of UT Southwestern Medical Center, and Jochen Zimmer of University of Virginia School of Medicine, on being among the 33 newly-announced 2021 HHMI Investigators.

We have an internal congrats to offer as well, to SBGrid staff member Pavel Filipčík, from our New Zealand outpost at University of Otago, who is off to work on single molecule electron diffraction in the laboratory of Jan Pieter Abrahams at the University of Basel. We'll sorely miss Pavel's contribution to the technical team, compiling software, solving support tickets (often while the rest of our team slept), and lending his CryoEM expertise. We will soon have a job description posted to fill this vacancy, so please contact us if you know others in the region who might be interested in the position.

Many thanks to Alessandra Villa for helping us kick off our webinar series on Tuesday with an update on GROMACS. You can find a recording of her presentation on the SBGrid YouTube channel. We've filled out most of the dates for the remainder of 2021 (see October dates below), but always welcome your suggestions, so please be sure to let us know if you've got some exciting new research to present or are interested in learning more about a particular software title.

SBGrid Weekly Webinar Series

Oct 5: Kirill Nadezhdin and Arthur Neuberger, Sobolevsky Laboratory, Columbia University - Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel

Oct 12: Jim Vincent, Harvard Medical School - BioGrids for SBGrid Users

Oct 26: Johannes Elferich, Grigorieff Laboratory, University of Massachusetts Medical School - High-throughput in-situ cryo-EM of hematopoietic differentiation

Webinar details here

Our September SBGrid Tale took us to the barrier island of Galveston on the Texas Gulf Coast and the laboratory of Gabby Rundenko at University of Texas Medical Branch, whose penchant for tackling big problems is born of her belief in the power of first steps. Whether learning to drive by taking a solo road trip with from Seattle to Dallas, with natural wonder detours dotting her way, or taking structural biology to neuroscience, choosing mental illness as her domain when the proteins she needed to crystallize were not yet identified, Rudenko dives in and takes it step-by-step. [Read the full story].

This month's software push includes updates to CCP4, GROMACS, HOMER, and RELION (x2), and one new title: HMMER. See Software Changes below for complete details.

Eight new members joined SBGrid in September: Scott Blanchard from St. Jude Children's Hospital, Elena Harjes from Massey University in Palmerston North, New Zealand, Debajyoti Dutta of the Thapar Institute of Engineering and Technology in Punjab India, and five groups from the University of Colorado, Boulder: Halil Aydin, Thomas Cech, Vignesh Kasinath, Karolin Luger, and Chuck Moe. Welcome to our newest members!

Technical notes from our Software Team

Installation Manager auto-update: Our GUI installation manager now has auto-update functionality, allowing you to update the installation manager directly from the “SBGrid Installation Manager” menu in the top left with no need to download new versions from our website. This feature is available in version 2.4.0 and later for Mac and Linux computers.

Community Announcements

SBGrid Australasian III Webinar Series: We're excited to announce our third Australasian regional mini-series, this time with a focus on cryo-electron microscopy. With five lectures and nine speakers this session should appeal to both novice and expert structural biologists.

Wednesdays at 12pm - Oct 27-Nov 24 (all dates/times New Zealand Time).

Drs. Kurt Krause (U. Otago), Piotr Sliz (Harvard Medical School), and Antoine van Oijen (U. Wollongong) will host this series of one-hour sessions to include an opening keynote from Prof. Yifan Cheng, a special lecture from Prof. Tamir Gonen, a panel discussion on sample preparation (single particle cryoEM to MicroED, tomography and FIB milling), presentations on effective on-the-fly data processing and using AlphaFold with ChimeraX, a review of MicroED past and future, and a closing panel on regional CryoEM infrastructure in Australasia from data collection to analysis.

We're finalizing the speaker list now, and will soon announce the full schedule and registration details.

Member Publications

Over 100 new member publications appeared in journals this month. You can find a complete listing on our website, along with a couple of notable highlights below:

•

A new eLife paper from Thomas Schalch's laboratory at the University of Leicester documents the authors' investigation into the mystery of how the SUV39 class of methyltransferase enzymes designate specific genomic regions as heterochromatic. The study focuses on the fission yeast Schizosaccharomyces pombe heterochromatin system and its SUV39 protein Clr4. [Abstract]

•

In Biochemistry, UMass Chan Medical School's Celia Schiffer presents crystal structures of the pan-3C protease inhibitor rupintrivir bound to SARS-CoV-2's enterovirus 68 3C protease and 3C-like main protease. Examination of the structures led to the discovery that rupintrivir attaches itself to the active site of SARS-CoV-2 main protease in a unique way, dividing the catalytic cysteine and histidine residues.

[Abstract]

•

From our graduate student desk, Harvard student Kristen Rodrigues highlighted a study that appeared Science from Sebastian Klinge's laboratory at The Rockefeller University, in which the authors present the structures of three states of the human SSU processome, obtained using a human genome editing platform they developed to biallelically affinity tag the endogenous SSU processome, then isolate it from the nucleolus. [Read more].

Deposit your experimental datasets: If you're currently preparing a manuscript, please remember that, while you're making the PDB record deposit and publication submission, you can also preserve your primary experimental datasets with deposits to the SBGrid Data Bank.

Acknowledge SBGrid: SBGrid operations are funded with member fees and grants, so we are grateful when you are able to acknowledge SBGrid in your presentations and publications.

Please use this SBGrid logo on the acknowledgements slide of your presentations.

We recommend the following boilerplate language for inclusion in publications that report results obtained with SBGrid supported software:

Structural biology applications used in this project were compiled and configured by SBGrid [1].

[1] A. Morin, B. Eisenbraun, J. Key, P. C. Sanschagrin, M. A. Timony, M. Ottaviano, and P. Sliz, “Collaboration gets the most out of software.,” Elife, vol. 2, p. e01456, Sep. 2013.

Link to article: https://elifesciences.org/articles/01456.

SBGrid citations: SBGrid's eLife paper received 5 new citations in the month of September, in publications that include these current and former SBGrid-member laboratories: George Phillips from Rice University in Acta Crystallographica Section F: Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis;

Melanie Ohi of University of Michigan and Borden Lacy at Vanderbilt University in Infection and Immunity: Functional properties of oligomeric and monomeric forms of Helicobacter pylori VacA toxin; Sandra Gabelli at Johns Hopkins University School of Medicine in Nature Communications: Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens; and John Kuriyan at University of California, Berkley in Cell: Structural basis and regulation of the reductive stress response. And from former member Holger Sondermann, now at Christian-Albrechts-University of Kiel, in Journal of Cell Biology: The hypervariable region of atlastin-1 is a site for intrinsic and extrinsic regulation.

Thanks for remembering us!

Software Changes

CCP4 7.1.016 includes updates to COOT, CCP4cloud, ccp4i2, phaser, mrbump, privateer, rabdam, morda, and monomers.

GROMACS 2021.3 fixes a number of bugs.

HOMER 4.11 adds routines for csRNA-seq (TSS) analysis.

HMMER is new to SBGrid at version 3.3.2. HMMER uses probabilistic models called profile hidden Markov models (profile HMMs) to search sequence databases for sequence homologs and to make sequence alignments.

RELION 3.1.3 is the new default and includes compatibility fixes for CUDA 11.5 and Intel oneAPI SDK, with more details in the installation manual and the note: "Do Not use environment variables CC, CXX, MPICC, MPICXX." This update also fixes race conditions in local scratch, buffer overflow in FileName::compose, and an EER defect in Bayesian Polish. Other changes: relion_convert_to_tiff: treats MODE 0 MRC as signed and MotionCorr treats pixels with zero gain as defects even in non-EER movies.

AND RELION 4.0 beta is also now available via version override. This version contains a new approach to subtomogram averaging #teamtomo, improved 2D classification, automated 2D class selection, and an improved framework for on-the-fly processing.

Please note that not all software applications are available to every SBGrid member type. If you see an application that you would like to use, but is not included in your software tree, please contact us to find out what options are available for access.

This newsletter is sent to you because you are a member or affiliate of the SBGrid Consortium, the Structural Biology Grid computing consortium.

More information about the SBGrid Consortium is available at https://sbgrid.org

Report software bugs: sbgrid.org/bugs

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