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.

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.