forthcoming articles

In a pilot study, K-edge anomalous SAXS signal was obtained from a small dimeric protein containing poly histidine tags bound to cupric ions, which can be used for the assessments of protein structural models in solution.

A perspective on the future development of Real-Space methods in cryo-EM.

This study determine the first structure of a novel archaeal-like Holliday junction resolving enzyme originating from a thermophilic phage, and demonstrates its function, cleaving X-shaped dsDNA. Furthermore, a novel signature motif for Holliday junction resolving enzymes originating from thermophilic bacteriophages is proposed.

Although cryo-electron microscopy has revolutionized structural biology, its applicability to high-resolution structure analysis of comparatively small enzymes is so far largely unexplored. We report on two cryo-EM structures of ~120 kDa plant borneol dehydrogenases at or below 2 Å resolution.

Urate oxidase structures under high hydrostatic pressure per se and high argon pressure have been analyzed, deciphering the basis of the protein-ligand stabilization by pressure and the formation of a transient intermediate dimeric sub-state during the pressure-induced dissociation.

It is shown that the inclusion of glycerol in single-particle cryoEM buffers does not preclude high-resolution structure determination, as demonstrated by a ∼2.3 Å reconstruction of mouse apoferritin (∼500 kDa) and a ∼3.3 Å reconstruction of rabbit muscle aldolase (∼160 kDa) in the presence of 20%(v/v) glycerol.

The implications of the AlphaFold2 protein structure modelling software for crystallographic phasing strategies are discussed.

The types, scopes, availability and complementarity of databases for intrinsically disordered proteins are described.

The crystal structure of guanosine monophosphate synthase from A. fumigatus, an attractive antifungal drug target, reveals unique differences from the human homologue that can be effectively targeted.

A program utilizing artificial learning and convolutional neural networks, named Helcaraxe, has been developed which can detect ice-crystal artefacts in processed macromolecular diffraction data with unprecedented accuracy.

Contrary to expectations from orthologous structures in mouse and cow, a structure of holo human adenosine deaminase 1 shows that it adopts a closed conformation at the entry to its active site. This finding poses a cautionary tale for reliance on homologs for structural inference relevant to applications such as protein engineering or drug development.

An end-to-end supervised learning method to directly recover missing orientations from 2D cryo-EM images is described.

The crystal structure of YxaL was determined, revealing an eight-bladed β-propeller fold with a structural variation. The protein was subsequently engineered based on the structure, resulting in an improved plant growth-promoting activity.

The accuracy of B factors, estimated by comparing the same atoms in numerous protein crystal structures, is rather modest: close to 9 Ų in ambient-temperature structures and to 6 Ų in low-temperature structures. These values are similar to those estimated two decades ago, indicating that little has changed since.

Ten goals for the future development of macromolecular refinement programs are described.

In this study, the crystal structure of anti-CRISPR-associated 2 (Aca2) was solved and it was shown that Aca2 forms dimers in solution, which are critical for promoter binding; specific residues that are critical for DNA binding and their conservation were revealed. Since the mechanism of action is largely conserved among different Aca protein families, insights are provided into their structure and function.

The key factors that should be considered during the planning and execution of a time-resolved crystallographic experiment are discussed, with a focus on time-resolved serial synchrotron crystallography.

The binding properties of two drug-like fragments to a conformationally dynamic site in disulfide bond-forming protein A from B. pseudomallei are described.

High-resolution X-ray diffraction data were collected at room temperature for light- and dark-adapted states of the archaerhodopsin-3 photoreceptor using transparent and opaque polymer-film sample mounts.

A quinary multi-hexameric helical structure of T. cruzi NDPK1 is supported by crystallographic and in vivo studies.

The new CAB automatic model-building program is described and compared with other automated model-building techniques.

A standalone system, called PDB-Dev, has been developed for archiving integrative structures and making them publicly available. The paper describes the data standards, the software tools and the various components of the PDB-Dev data-collection, processing and archiving infrastructure.

New restraints for the nitroxide radical ligand MTN defined based on quantum-chemical computations allow the accurate re-refinement of protein structures.

A machine-learning model was used to predict the performance of four crystallographic model-building pipelines (ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE) and their combinations.

A 3D cellular imaging platform developed at beamline B24 at Diamond Light Source has been used to identify cellular features such as filamentous actin in mammalian cells. This approach enabled virtual same-sample imaging of structures captured on separate microscopes through rigid transformation of 3D data in silico, bypassing the need for additional sample processing and ensuring artefact-free data correlation.

The crystal structure of the A. muciniphila arylsulfatase AmAS is reported and some structural regularity of substrate binding and specificity was noted. Insights into the catalytic mechanism of mucin-desulfating sulfatases in A. muciniphila are also provided based on this regularity.