Take a look at our latest issue: journals.iucr.org/d/issues/202...

On the cover: detemination of the crystal structure and nickel-binding capacity of the Proteus mirabilis virulence factor UreE allowed the assignment of putative nickel-binding sites doi.org/10.1107/S205...

Take a look at our latest issue: journals.iucr.org/d/issues/202...

On the cover: detemination of the crystal structure and nickel-binding capacity of the Proteus mirabilis virulence factor UreE allowed the assignment of putative nickel-binding sites doi.org/10.1107/S205...

The structure of the NTR domain of NADPH-dependent thioredoxin reductase C identifies two Cys residues crucial for the intrinsic stability of its complex with 2-Cys peroxiredoxin #NADPHDependentThioredoxinReductaseC #CysPeroxiredoxin #XRayDiffraction doi.org/10.1107/S205...

A novel system is presented that enables the association of text mentions of functionally important residues with their corresponding counterparts in a PDB entry and reference UniProt accession #TextMining #LargeLanguageModels #TextAnnotations doi.org/10.1107/S205...

ICECREAM: high-fidelity equivariant cryo-electron tomography We present ICECREAM, a self-supervised approach that achieves substantially better denoising and more reliable missing-wedge recovery in cryo-ET, while reducing training and inference time relative to comparable baselines.

Vinith Kishore et al.: ICECREAM: high-fidelity equivariant cryo-electron tomography #CryogenicElectronTomography #SelfSupervisedLearning #MachineLearning @insadelyon...#IUCr https://journals.iucr.org/paper?S2059798326001622

Single numerical descriptors of cryo-EM view distribution non-uniformity are proposed which can serve as a concise reference value for reporting and database annotation #CryoEM #AngularDistributionOfViews #NonUniformDistribution doi.org/10.1107/S205...

Crystal structures of Fsc1, a novel autophagy factor that mediates autophagosome–vacuole fusion in fission yeast Crystal structures of the autophagy protein Fsc1 reveal conserved fasciclin features and a stable dimer interface that illuminate its possible role as a scaffold in autophagosome–vacuole membrane fusion.

Azuka, Liu and Jin: Crystal structures of Fsc1, a novel autophagy factor that mediates autophagosome–vacuole fusion in fission yeast #Fsc1 #FasciclinDomain #AutophagosomeVacuoleFusion @michiganstateu...#IUCr https://journals.iucr.org/paper?S205979832600197X

SAXS studies of four 60 bp DNA duplexes with sequences closely related to part of the GAGE6 promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA–protein binding #DNABending #SAXS doi.org/10.1107/S205...

The results of 3D reconstructions using an explicit correction of the number of overrepresented and underrepresented projections for non-uniformly distributed sets are reported #CryoEM #3DReconstruction #ViewFrequency doi.org/10.1107/S205...

Protein structure of a glycoside hydrolase family 30, subfamily 12 endo-1,4-β-xylanase This report describes the first protein structure from a new glycoside hydrolase family 30 subfamily which specifically degrades the biomass-derived polysaccharide xylan.

Franz J. St John et al.: Protein structure of a glycoside hydrolase family 30, subfamily 12 endo-1,4-β-xylanase #GlycosideHydrolaseFamily30 #GH30 #GH3012 @UChicago...#IUCr https://journals.iucr.org/paper?S2059798326002160

This Scientific Comment suggests that the PDB should use the CAVEAT option much more prominently to warn consumers about potential risks and errors in its archives #MacromolecularStructureQuality #ArtificialIntelligence #DataMining doi.org/10.1107/S205...

AXIS: a Lab-in-the-Loop machine learning approach for automated detection of macromolecular crystals AXIS (AI-based Crystal Identification System) combines artificial intelligence with an iterative Lab-in-the-Loop approach for automated crystal detection. AXIS ensures high performance in crystal detection, requires small training datasets and facilitates rapid adaptation to local and changing conditions at any given facility.

Aurelien Personnaz et al.: AXIS: a Lab-in-the-Loop machine learning approach for automated detection of macromolecular crystals #StructuralBiology #AI #LabInTheLoop ... #IUCr https://journals.iucr.org/paper?S2052252526001399

Molecular analysis of 3D domain swapping in the acylphosphatase from Escherichia coli Structures of the monomer and intertwined dimer of the acylphosphatase from E. coli shed light on the molecular basis of its 3D domain swapping.

Sergio Martínez-Rodríguez et al.: Molecular analysis of 3D domain swapping in the acylphosphatase from Escherichia coli #Acylphosphatases #ProlineIsomerization #3DDomainSwapping @canalugr@ualmeria...#IUCr https://journals.iucr.org/paper?S2059798326001774

Automated workflows for strategy computation and data collection at synchrotron beamlines This paper presents and explains a workflow program for automatically deriving, optimizing and executing complex multi-sweep diffraction experiments for macromolecular crystallography at synchrotron beamlines.

Rasmus H. Fogh et al.: Automated workflows for strategy computation and data collection at synchrotron beamlines #MacromolecularXRayCrystallography #ExperimentalStrategy #Automation ... #IUCr https://journals.iucr.org/paper?S2059798326001920

New structural insights into the molecular determinants of the substrate specificity of ADAMTS-5 underscore the spacer domain as a promising target for the development of selective inhibitors #SpacerDomain #Aggrecanase #Osteoarthritis doi.org/10.1107/S205...

The crystal structure of the hydroxycinnamoyl transferase EpHTT offers insights for the metabolic engineering of chicoric acid production #EpHTT #HydroxycinnamoylTransferases #EchinaceaPurpurea doi.org/10.1107/S205...

The new Leopard-EM software package for 2D template matching has been written with extensibility at the forefront #InSituStructuralBiology #CryoEM #CryoET doi.org/10.1107/S205...

Very excited that the first publication from my lab is now online! Thanks to @actacrystd.iucr.org editors and reviewers for the smooth publication process. And congratulations to first author, Jiayi Pan, who completed this work in her Master’s year! @biologyanu.bsky.social

Bayesian perspective for orientation determination in cryo-EM with application to structural heterogeneity analysis A Bayesian perspective on orientation estimation in cryo-EM is presented, with the minimum mean-square error estimator outperforming standard cross-correlation-based approaches, particularly under challenging low signal-to-noise conditions. We demonstrate that improved orientation estimation has a decisive impact on 3D reconstruction quality and structural heterogeneity recovery.

Sheng Xu et al.: Bayesian perspective for orientation determination in cryo-EM with application to structural heterogeneity analysis #BayesianInference #CryoElectronMicroscopy @princeton@telavivuni1...#IUCr https://journals.iucr.org/paper?S2059798326001415

Molecular structure and nickel-binding capacity of Proteus mirabilis UreE This study presents a 2.0 Å resolution crystal structure and determined the nickel-binding capacity of the P. mirabilis nickel chaperone UreE. UreE is essential for the delivery of nickel to the metalloenzyme urease, which is key for the ability of P. mirabilis to cause urinary-tract infections.

Jiayi Pan et al.: Molecular structure and nickel-binding capacity of Proteus mirabilis UreE #Metalloproteins #NickelChaperones #ProteusMirabilis @ANUmedia...#IUCr https://journals.iucr.org/paper?S2059798326001907

A new macromolecular crystallography endstation, MX-ES, has been established at NanoTerasu, Japan's first fourth-generation synchrotron-radiation facility #NanoTerasu #MacromolecularCrystallography #IntegratedStructuralAnalysisPlatform doi.org/10.1107/S205...

Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection - PubMed The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in…

News Alert: We've updated SBGrid's primary citation to our 2024 Acta Crystallographica paper. We would be grateful if you could use this reference in future manuscripts, preprints, and related work where appropriate.

Read it here: buff.ly/RQ0Ybpx

#SBGrid #Citation

Take a look at our March issue: journals.iucr.org/d/issues/202...

On the cover: the response of two paradigmatic metalloproteins of different types, one iron-containing and one copper-containing, to X-ray-induced metal reduction at cryo- and room temperature journals.iucr.org/d/issues/202...

Q-score as a reliability measure for atomic coordinate models

Q-scores are calculated for atomic models derived from 3D electron microscopy maps, measure how well the model fits the map and reflect the quality of the map itself.

🔗 Find out more:
https://ow.ly/4Vkx50Ynrxi

@ucsandiego @ActaCrystD @IUCr #CryoEM #QScores #Validation

PDB Reaches a New Milestone The PDB now contains more than 250,000 entries

PDB Reaches a New Milestone: more than 250,000 entries

Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples Cryo-EM analysis of apoferritin exposed to an X-ray dose of 100 MGy confirms the potential for high-resolution correlative imaging workflows combining X-ray tomography and cryo-EM.

Thorsten B. Blum et al.: Radiation-dose effects in correlative X-ray/cryo-electron microscopy of frozen-hydrated biological samples #CryoXRayTomography #CryoElectronMicroscopy #CorrelativeMicroscopy @eth...#IUCr https://journals.iucr.org/paper?S2059798326001427

An optimized data-acquisition and processing strategy for the collection of high-quality electron diffraction data from extended crystals using conventional cryo-EM instrumentation #ElectronDiffraction #RadiationDamage #DataCompleteness doi.org/10.1107/S205...

This topical review considers a Protein Data Bank and Cambridge Structural Database data survey of crystal structures that have been determined at elevated temperatures #BodyTemperature #PhysiologicalConditions #37C doi.org/10.1107/S205...

A theoretical framework for the development of dynamic nuclear polarization neutron macromolecular crystallography to advance the resolution of H atoms within biomolecular crystals is presented #DynamicNuclearPolarization #PhaseRetrieval #Hydrogen doi.org/10.1107/S205...

X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides X-ray exposure influences the structures of Cu(I), Cu(II) and Zn(II) complexes of amyloid-β (Aβ) peptides in different ways. While Cu(I) and Zn(II) complexes show no detectable X-ray-induced spectral changes, Cu(II) complexes undergo significant spectral evolution under irradiation. Experiments on the truncated fragments Aβ1–6 and Aβ1–16 show that the extent of relaxation depends on the peptide length, on the binding mode and on the temperature.

Bharath Vinjamuri et al.: X-ray beam effects on metallo-peptides reflect redox events: insights from X-ray absorption spectroscopy measurements on metal complexes of truncated amyloid-β peptides @UGrenobleAlpes...#IUCr https://journals.iucr.org/paper?S2059798326001348