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 7 June 2023

The structure of the RBD–E77 Fab complex reveals neutralization and immune escape of SARS-CoV-2

E77 antibody with high binding affinity to prototype and Delta RBD was identified. The RBD/E77-Fab complex structure shows that E77 antibody mimics the binding of ACE2 to RBD and N501Y mutation from VOCs abolishes the binding potency of E77 to RBD.

Accepted 7 June 2023

Overall protein structure quality assessment using hydrogen-bonding parameters

A new protein structure validation method using hydrogen bonding parameters is described.

Accepted 6 June 2023

Module walking using an SH3-like cell-wall-binding domain leads to a new GH family of muramidases

We describe the identification, characterization and X-ray structure of a novel fungal GH24 muramidase from Trichophaea saccata in which a SH3-like cell wall binding domain (CWBD) was identified by structure comparisons, in addition to its catalytic domain. A domain walking approach was then used to identify a group of fungal muramidases belonging to a new GH family, containing homologous SH3-like cell wall binding modules and we report the X-ray structures of the independent catalytic and SH3-like domains of three of them.

Accepted 5 June 2023

Raynals, an online tool for the analysis of dynamic light scattering

Raynals is an online, user-friendly, free (for academia) and advanced tool for the analysis of single-angle dynamic light scattering data. The estimation of the size distribution is done through the Tikhonov-Phillips regularization.

Accepted 30 May 2023

3D structures of the Plasmodium vivax SUB1 subtilisin-like drug target reveal conformational changes to accommodate a substrate-derived α-keto-amide inhibitor

In this work, Martinez et al. describe the first high-resolution 3D structure of Plasmodium vivax SUB1 complexed with a substrate-derived pseudo-peptide inhibitor. Subtle conformational changes in the enzyme-inhibitor complex define new pharmacophores for iterative cycles of structure-driven synthesis to accelerate the discovery of optimized SUB1 inhibitors that could represent a new generation of anti-malarial candidates.

Accepted 30 May 2023

Crystal structure of di­hydrofolate reductase from the emerging pathogenic fungus Candida auris

The first structures of C. auris dihydrofolate at near-atomic resolution are described, including apo and holo forms and complexes with two antifolate drugs: pyrimethamine and cycloguanil. C. auris is a highly significant globally emerging and resistant fungal pathogen and there is a great demand for research and progress towards novel therapeutics.

Accepted 26 May 2023

Conformation-based refinement of 18-mer DNA structures

The refinement and validation of nine A-form DNA 18-mer crystal structures containing both canonical and noncanonical base pairs benefits from using dinucleotide conformational classes (NtCs).

Accepted 22 May 2023

Thermostable homologues of the periplasmic siderophore-binding protein CeuE from Geobacillus stearothermophilus and Parageobacillus thermoglucosidasius

The expression, characterization and structures of CeuE homologues from two thermophilic bacteria, G. stearothermophilus and P. thermoglucosidasius, are described together with their ligand binding. The proteins show enhanced thermostability and resistance to organic chemicals; consequently, these thermophilic homologues offer advantages in the development of artificial metalloenzymes using the CeuE family.

Accepted 22 May 2023

Scipion Flexibility Hub: an integrative framework for advanced conformational heterogeneity analysis in cryoEM

Accepted 22 May 2023

Direct phasing algorithm for protein crystals with high solvent content using low-resolution diffraction data

In this work, a novel method to recover the diffraction phase independently using the low-resolution data is proposed and it has been verified and found to be useful and practical using several typical examples. In addition, a practical metric has been established to determine whether the algorithm converges to a correct solution by estimating the entropy of the final results.

Accepted 15 May 2023

Structural basis of regioselective tryptophan dibromination by the single-component flavin-dependent halogenase AetF

The single-component flavin-dependent tryptophan halogenase AetF converts tryptophan to 5,7-dibromotryptophan during the biosynthesis of the neurotoxin aetokthonotoxin. Crystal structures of AetF with the substrates tryptophan and 5-bromotryptophan show that a flip of the indole moiety of tryptophan positions first C5 and then C7 in the same location in the active site to facilitate two successive bromination reactions.

Accepted 14 May 2023

Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.

The crystal structure of the monocupin 5-nitrosalicylate 1,2-dioxygenase, an iron(II)-dependent ring-cleaving dioxygenase, from Bradyrhizobium sp. was determined by molecular replacement using a theoretical model obtained by AlphaFold2. Comparison with structures of other members of the same class and docking of the substrate allowed identification of the residues responsible for its very unusual enzyme selectivity.

Accepted 12 May 2023

Structure–function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role

The crystal structure of a novel laccase-like multicopper oxidase from the thermophilic fungus T. thermophila was refined at 1.9 Å resolution. Ligand-docking simulations reveal conformational changes that influence substrate specificity.

Accepted 2 May 2023

Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis

Structures of mannose 2-epimerase and a mutant from R. slithyformis were determined in their apo form and in complex with D-glucitol. In combination with a biochemical assay, the molecular basis of the substrate specificity and activity of the enzyme was elucidated.

Accepted 28 April 2023

Protein–macrocycle polymorphism: crystal form IV of the Ralstonia solanacearum lectin–sulfonato-calix[8]arene complex

Calixarene-mediated protein assembly provides a basis for the development of new types of biomaterials. A fourth structure of the R. solanacearum lectin–sulfonato-calix[8]arene complex expands the crystal-engineering landscape and suggests an alternative pH trigger of assembly.

Accepted 26 April 2023

Sequence-assignment validation in protein crystal structure models with checkMySequence

It is shown that checkMySequence, an automated method for validating sequence assignment in cryo-EM structures of proteins, can be used to validate crystal structure models.

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