RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The RCSB PDB research-focused web portal at https://www.rcsb.org/ provides important tools and resources to search, visualize and analyze experimentally determined 3D biostructures alongside computed structure models of proteins predicted using artificial intelligence/machine-learning based tools.

Chaperone-mediated MHC-I peptide exchange in antigen presentation

This topic review summarizes structures of chaperones complexed with MHC-I, the structural principles that govern peptide exchange and the mechanism in antigen presentation.

The ABC toxin complex from Yersinia entomophaga can package three different cytotoxic components expressed from distinct genetic loci in an unfolded state: the structures of both shell and cargo

A cytotoxin encoded by an `orphan' genetic locus in the insect pathogen Yersinia entomophaga is shown to be a functional part of an ABC toxin complex, and the structures of both the RHS-repeat-containing `shell' and the free toxin alone are determined by X-ray crystallography. The structure of the toxin indicates that it most likely functions by directly modifying actin in the target cell.

Dynamical refinement with multipolar electron scattering factors

Transferable aspherical atom model dynamical refinement on precession electron diffraction data for 1-methyl­uracil crystals offers superior performance compared with the independent atom model and reveals that the quality of 3D electron diffraction data and dynamical refinement is already sufficient to detect minute variations of the electrostatic potential caused by bonding and intermolecular interactions.

Nanostructure and dynamics of N-truncated copper amyloid-β peptides from advanced X-ray absorption fine structure

An X-ray absorption spectroscopy electrochemical cell was used to collect high-quality X-ray absorption spectroscopy measurements of N-truncated Cu:amyloid-β (Cu:Aβ) samples under near-physiological conditions. The geometry of binding sites for the copper binding in Aβ_4–8/12/16 and the ability of these peptides to perform redox cycles in a manner that might produce toxicity in human brains were determined.

Linking solid-state phenomena via energy differences in `archetype crystal structures'

Solid-state phenomena like disorder, polymorphism but also the occurrence of high-Z′ crystal structures can be linked via energy differences in `archetype crystal structures', which will permit better prediction of their occurrence.

Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development

A detailed analysis of rhenium(I) organometallic covalent binding to a model protein is conducted at seven time points over 38 weeks. Changes in the protein structure induced at the Re binding sites over the time series as well as the relationship between the proximity of the solvent channels to the residues containing the highest-occupied Re are described.

Biophysical and structural study of La Crosse virus endonuclease inhibition for the development of new antiviral options

A structural analysis of several metal-ion binders that inhibit viral endonucleases is performed.

Structural insights into the molecular mechanism of phytoplasma immunodominant membrane protein

The first crystal structure of phytoplasma immunodominant membrane protein is reported and structural analysis revealed its potential for actin binding.

Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity

The human peptidylarginine deiminase type VI (PAD6) is essential in oocyte and embryonic development as a component of the supramolecular assemblies called cytoplasmic lattices. The crystal structure presented here suggests PAD6 assembles as a dimer resembling other PADs, albeit with compromised abilities to bind Ca²⁺ and substrates. This aligns with existing in vitro data which indicate an enzymatically inactive isoform of PAD.