SBGrid's eLife paper received a citation in May from K. Christopher Garcia at Stanford University School of Medicine in Nature Biotechnology: Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery.
Read more here: https://doi.org/10.1038/s41587-026-03128-x
New Title Alert: xds-zcbf- is a XDS plugin for fast reading of cbf.gz files. The plugin eliminates the need for multiple file system accesses by way of direct calls to zlib.
More here: https://git.embl.org/nikolova/xds-zcbf
SBGrid's eLife paper received a citation in May from Brandt Eichman at Vanderbilt University in EMBO Reports: DNA binding and lesion recognition by the bacterial interstrand DNA crosslink glycosylase AlkX.
Interstrand DNA crosslinks (ICLs) are a highly toxic form of DNA damage. ICL repair in both eukaryotes and bacteria involves unhooking of the two strands by specialized DNA glycosylases. We recently established that the human pathogen Acinetobacter baumannii contains an ICL glycosylase (AlkX) that facilitates pathogenesis and protects the bacteria from DNA damage and acid stress. However, the physical basis for glycosylase-catalyzed ICL unhooking is unknown. Here, we describe a crystal structure of AlkX bound to DNA representing a product of the ICL unhooking reaction. Mutational analysis of ICL unhooking in vitro and A. baumannii sensitivity to the crosslinking agent mechlorethamine enable the identification of several AlkX motifs critical for ICL repair. We also find that a genetic variant from an antibiotic-resistant strain of the human pathogen Salmonella enterica reduces AlkX activity in vitro and increases A. baumannii sensitivity to DNA crosslinking. This work provides a structural basis for how bacterial ICL glycosylases recognize and repair DNA adducts and contributes additional evidence that ICL repair is important for fitness of human pathogens.
Community Announcements:
Upcoming event from our partners at Instruct-ERIC
Instruct Course on Calorimetric and Spectroscopic Characterization of Biomolecules
Sept 7-11, 2026 | Brno, Czechia
Organized in collaboration with Anamet and Specion
Register here: https://www.ceitec.eu/instruct-course-on-calorimetric-and-spectroscopic-characterization-of-biomolecules/a5545
SBGrid's eLife paper received a citation in May from Seth Darst at The Rockefeller University in Molecular Cell: Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity.
Technical Notes: May's software push includes updates to AlphaFold3, autoPROC, BoltzGen, Buster, CCP4, ChemEx, COOT, cryoCAT , DIALS, Maxit, MotionCor3, OpenFreeEnergy, OpenMM, PowerFit, pytom-match-pick, TOMOMAN, Topaz, Volume_Seg_Tool, and Warp.
More here: https://sbgrid.org/software/recent/archive/2026/05/
Meharry Medical College student Mudiare Ikoba highlighted a publication that appeared in Science Advances from SBGrid member Huanhuan Joyce Chen and colleagues at The University of Chicago, exploring the mechanism underlying pulmonary neuroendocrine cells’ response to oxidative stress.
Read more here: https://medium.com/sbgrid-community-news/uncovering-a-lung-to-brain-pathway-for-nicotine-induced-neural-stress-6d3034d3e15d
Fisk University student Cariuna Ellison's highlight features a Nature Communications publication from the laboratory of Crina Nimigean at Weill Cornell Medicine in which the authors describe the precise conditions and resulting mechanisms that result in thermosensitivity in a bacterium.
Read more here: https://medium.com/sbgrid-community-news/not-too-cold-just-right-19ebb647354e
In case you missed Jarrett Johnson's presentation on visualization and CryoEM in PyMOL in May, you can watch the recording on the SBGrid YouTube Channel.
More here: https://youtu.be/IxWcDX5nSgY
SBGrid's eLife paper received a citation in April from Antonina Roll-Mecak from the The National Institutes of Health in Journal of Cell Biology: Insights into retinal disease and non-tubulin glutamylation from a RPGR–TTLL5 complex structure.
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