Structural Biology

QwenCryoMarker is a universal post-processing framework that converts the outputs of arbitrary particle pickers into clean, high-precision particle sets #CryoEM #ContaminationMarking #VisionLanguageModel doi.org/10.1107/S205...

To understand T-cell recognition of cancer neoantigens at the atomic level, a T-cell receptor that recognizes a neoepitope arising from a driver mutation in the p53 oncogene presented by HLA-A2 was studied #TCellReceptors #CancerNeoantigens #MHC doi.org/10.1107/S205...

The room-temperature serial synchrotron X-ray crystallography structure of Nitratidesulfovibrio vulgaris formate dehydrogenase AB is compared with previously reported cryogenic structures #CO2Reduction #MetalDependentFormateDehydrogenases #MoWEnzymes doi.org/10.1107/S205...

How does the bacterium behind brucellosis builds its protective `iron cage'? #Bacterioferritin #BrucellaMelitensis #Oligomerization doi.org/10.1107/S205...

A method for rapidly depositing, thinning and vitrifying samples for cryoEM on the sub-millisecond timescale #CryoEM #TimeResolvedCryoEM #StructuralBiology doi.org/10.1107/S205...

The determination of the highest resolution structure in the PDB at 0.43 Å resolution is described #SubMacromolecularCrystallography #AsphericalAtomModel #DeformationDensity doi.org/10.1107/S205...

Recent structural, functional and dynamic research on the bacterial melibiose permease MelB has revealed significant insights into the symport mechanisms of Na+-coupled MFS transporters #CryoEM #XRayCrystallography #HDXMS doi.org/10.1107/S205...

A practical approach for ligand validation during structure determination is outlined and key pitfalls are illustrated by re-examining several deposited PDB entries #LigandValidation #XRayCrystallography #StructureGuidedDrugDiscovery doi.org/10.1107/S205...

The Guest Editors introduce the special issue based on talks at the CCP4 Study Weekend 2024 #CCP4StudyWeekend #DecisionMaking #MacromolecularCrystallography doi.org/10.1107/S205...

A crystal form of tankyrase 2 that can be used efficiently in replacement soaking (also known as cross-soaking) when tankyrase 2 is co-crystallized with a low-affinity inhibitor is described #ReplacementSoaking #DrugDesign #Tankyrase doi.org/10.1107/S205...

LowDoseWizard addresses a practical limitation of routine cryo-TEM operation by reducing the setup of low-dose imaging conditions to a guided and standardized workflow implemented in SerialEM #LowDoseImaging #SerialEM #CryoEM doi.org/10.1107/S205...

In order to accommodate the tremendous growth of the PDB, it has become necessary to extend the identifiers of structures from 4 to 12 characters and adjust how data are organized in the archive #ProteinDataBank #PDB #MacromolecularStructure doi.org/10.1107/S205...

Structures of KPT-7523 bound to PAK4 and NAMPT provide a structural framework for the rational design of next-generation dual inhibitors targeting oncogenic signaling and metabolic pathways #PAK4 #NAMPT #KPT7523 doi.org/10.1107/S205...

The structure of endo-β-1,6-galactanase is the first reported of a GH30 subfamily 5 enzyme, providing structural insights into the molecular basis of β-1,6-galactan recognition in the catalytic cleft #EnzymeSubstrateComplex #GlycosideHydrolaseFamily3 doi.org/10.1107/S205...

A short history of Auto-Rickshaw @ActaCrystD @IUCr #AutoRickshaw #ExperimentalPhasing #MolecularReplacement doi.org/10.1107/S205...

Crystal structures of the pilus-specific sortase from Enterococcus faecalis provide insights into loop dynamics and substrate recognition and expands our understanding of sortase-mediated pilus polymerization #Enterococci #EbpPili #Sortases doi.org/10.1107/S205...

The prion-like domain from the plant thermosensory protein EARLY FLOWERING 3 was used as a model hydrogel for structural characterization by SAXS #LiquidLiquidPhaseSeparation #EARLYFLOWERING3 #SAXS doi.org/10.1107/S205...

A fully automated, unattended pipeline for on-the-fly cryo-EM data processing is presented that serves as a robust diagnostic tool for high-throughput facility environments #CryoEM #SPA #OnTheFlyProcessing doi.org/10.1107/S205...

Apologies for the incorrect link: the correct link is doi.org/10.1107/S205...

After analyzing 72 structures of NcAA9D, it was found that X-rays progressively reduce the active-site copper from Cu(II) to Cu(I), forming an electron-density feature that is easy to misinterpret #RadiationDamage #LPMOs #DioxygenBinding doi.org/10.1107/S205...

LsAA9A crystals were chemically reduced with or without saccharide substrate prior to low-dose X-ray data collection, revealing small but reproducible geometry differences across key states in the lytic polysaccharide monooxygenase catalytic pathway doi.org/10.1107/S205...

PETIMOT is a new neural network that learns to directly predict the most likely directions of motion for a protein from its sequence and 3D structure #ProteinFlexibility #MotionBenchmark #SE3EquivariantGNN doi.org/10.1107/S205...

SURFER is a lightweight, GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal #CryoEM #Segmentation #Membrane doi.org/10.1107/S205...

Crystal structures of AetF in complex with tryptoline and 8-bromotryptoline reveal the structural basis of regioselective halogenation and suggest two potential pathways to the formation of 6,8-dibromotryptoline #TryptophanHalogenases #Bromination doi.org/10.1107/S205...

The LRR crystallization screen described here enabled structure determination of the Arabidopsis receptor kinase SRF6 ectodomain #CrystallizationScreens #LeucineRichRepeats #Ectodomains doi.org/10.1107/S205...

Characterization of Dpo31 from the marine bacteriophage Carin-1 reveals that this protein displays a typical, although divergent, tail-spike protein fold #MarinePhages #Podoviruses #EPSDepolymerases doi.org/10.1107/S205...

Exploration of the acetyl-pyrrole scaffold led to the identification of BAZ2A-binding compounds assuming a peculiar, almost enclosed, conformation, as determined by X-ray crystallography #BAZ2A #Bromodomains #XRayCrystallography doi.org/10.1107/S205...

September issue is now available: journals.iucr.org/d/issues/202... The cover highlights the determination of the highest resolution structure in the PDB at 0.43 Å resolution. Electron-density maps reveal extensive deformation electron density. Read more at doi.org/10.1107/S205...

September issue is now available: journals.iucr.org/d/issues/202... The cover highlights the determination of the highest resolution structure in the PDB at 0.43 Å resolution. Electron-density maps reveal extensive deformation electron density. Read more at doi.org/10.1107/S205...

This paper was a nice side quest that started as a random encounter with @hrbridges.bsky.social at the poster session of the 2025 @ccpem.bsky.social Spring Symposium. It was very satisfying to finally see the macro domain of ALC1 that had escaped all previous structures of ALC1-nucleosome complexes!

Theoretical advances have led to a procedure for automatic solution of macromolecular structures with up to ~6000 non-H atoms in the ASU, resolutions up to 2.3 Å and heavy atoms in the unit cell #DirectMethods #PattersonMap #ProbabilisticApproach doi.org/10.1107/S205...

Monte Carlo neutron ray-tracing simulations of TOF–Laue neutron macromolecular crystal diffraction using the McStas software package were performed for the upcoming NMX Macromolecular Diffracto­meter at the European Spallation Source doi.org/10.1107/S205...

Direct structural evidence is provided for the complex of human citrate synthase and human mitochondrial malate dehydrogenase 2, which is part of the larger proposed citric acid cycle metabolon @JMU @uofsandiego #Metabolons #SAXS #MalateDehydrogenase doi.org/10.1107/S205...

Paper Published about the PDB Beta Archive Read about changes that will become the default on July 21, 2027. Transition to this new architecture today.

AlignPCA-2D is a principal component analysis-space Euclidean vector alignment method for fast, interpretable 2D classification in cryo-EM #3DReconstructionAndImageProcessing #SingleParticleCryoEM doi.org/10.1107/S205...

Studies using adenylate kinase provide guidelines for minimizing radiation artifacts in time-resolved X-ray solution-scattering experiments on multipurpose SAXS beamlines #TimeResolvedXRaySolutionScattering #SmallAngleXRayScattering #RadiationDamage doi.org/10.1107/S205...

A method for identifying potentially oxidatively damaged cysteines by interrogating the accuracy of the built model within the electron density and the geometry of the difference density peaks surrounding a cysteine #RadiationDamage doi.org/10.1107/S205...

🚨Get ready for the future of the PDB Archive! A new publication describes the PDB Beta Archive to support PDB users as they transition to the extended PDB ID and PDBx/mmCIF format. Start preparing for the July 21, 2027 transition. 📄Read here: journals.iucr.org/d/issues/202... #PDB

Through extensive classification of a previously deposited cryoEM dataset, a previously unresolved ALC1–nucleosome complex characterized by a more open conformation of ALC1 was identified #DNADamageResponse #ChromatinRemodeling #ALC1 doi.org/10.1107/S205...

The first reported crystallographic analysis of a β-lactamase in complex with the clinically relevant cephalosporin cefdinir was obtained using serial cryo-crystallography #SerialCrystallography #CTXM14 #Cefdinir doi.org/10.1107/S205...

The photoisomerization of the retinylidene protonated Schiff base in human retinol-binding protein II is described, along with the role of water molecules in this process #ProteinDesign #RhodopsinMimic #SingleCrystalPhotolysis doi.org/10.1107/S205...

📄New recommendations for fragment-screening data usage are here. The white paper summarizes community guidance on the deposition and reuse of structural biology data from fragment screening, hit-to-lead, and lead-optimization studies. ⬇️Read here ⬇️ cdn.rcsb.org/wwpdb/docs/d...

A new fusion tag can be used to solve a high-resolution structure of a GPCR by cryo-EM and resolve a small-molecule antagonist #GProteinCoupledReceptor #CryoEM #FusionTag doi.org/10.1107/S205...

The structure of PIP4K2A in complex with 422A, a potent dual PIP4K2A/2B inhibitor with improved metabolic stability, is used to define molecular features that govern isoform-dependent inhibitor binding within the PIP4K family #LipidKinases #PIP4K doi.org/10.1107/S205...

August issue is out! journals.iucr.org/d/issues/202... The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at doi.org/10.1107/S205...

August issue is out! journals.iucr.org/d/issues/202... The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at doi.org/10.1107/S205...

Out now in Journal of Applied Crystallography: mmCIF Validator, automated validation of mmCIF files against the PDBx/mmCIF dictionary Useful for structure deposition prep, biocuration, and automated QC (VS Code extension + Python/CLI) Paper: doi.org/10.1107/S160... Code: github.com/PDBeurope/mm...

A new type of article for Acta F: Protocols The purpose of this new category is to provide to the reader procedures that are sufficiently detailed so other researchers can reproduce the described workflow. Find out more in 'Show me how it's done: introducing Protocols': doi.org/10.1107/S205...