forthcoming articles

The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Structural Biology.

See also Forthcoming articles in all IUCr journals.

Accepted 23 November 2021

K-edge anomalous SAXS for protein solution structure modeling

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.

Accepted 19 November 2021

Real space in cryo-EM: the future is local

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

Accepted 19 November 2021

Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6

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.

Accepted 16 November 2021

CryoEM analysis of small plant biocatalysts at sub-2 Å resolution

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.

Accepted 15 November 2021

Comparison study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization

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.

Accepted 13 November 2021

A case for glycerol as an acceptable additive for single-particle cryoEM samples

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.

Accepted 13 November 2021

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

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

Accepted 12 November 2021

Databases for intrinsically disordered proteins

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

Accepted 11 November 2021

Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus

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.

Accepted 10 November 2021

Detecting ice artefacts in processed macromolecular diffraction data with machine learning

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.

Accepted 8 November 2021

Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation

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.

Accepted 5 November 2021

End-to-end orientation estimation from 2D cryo-EM images

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

Accepted 4 November 2021

Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering

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.

Accepted 4 November 2021

B-factor accuracy in protein crystal structures

The accuracy of B factors, estimated by comparing the same atoms in numerous protein crystal structures, is rather modest: close to 9 Å2 in ambient-temperature structures and to 6 Å2 in low-temperature structures. These values are similar to those estimated two decades ago, indicating that little has changed since.

Accepted 4 November 2021

Ten things I `Hate' about refinement

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

Accepted 4 November 2021

Molecular basis of transcriptional repression of anti-CRISPR by anti-CRISPR-associated 2

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.

Accepted 3 November 2021

Best practices for time-resolved serial synchrotron crystallography

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.

Accepted 29 October 2021

Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA

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

Accepted 26 October 2021

Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts

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.

Accepted 25 October 2021

X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure

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

Accepted 20 October 2021

Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program

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

Accepted 19 October 2021

New system for archiving integrative structures

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.

Accepted 18 October 2021

A radical approach to radicals

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

Accepted 10 October 2021

Predicting the performance of automated crystallographic model-building pipelines

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.

Accepted 6 October 2021

Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells

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.

Accepted 5 October 2021

Structural analysis of the sulfatase AmAS from Akkermansia muciniphila

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.

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