Submission of structural biology data for review purposes

The editors discuss the submission of structural biology data.

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.

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.

Ten things I `hate' about refinement

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

Structural and thermodynamic insights into a novel Mg²⁺–citrate-binding protein from the ABC transporter superfamily

MctA is an Mg²⁺-complexed citrate-binding protein from a Gram-negative bacterium that belongs to the ABC transporter superfamily. Comparison of the crystal structures of wild-type and mutant MctA proteins suggest a gating mechanism of substrate entry following an `asymmetric domain movement' mechanism of substrate binding.

Legionella effector LegA15/AnkH contains an unrecognized cysteine protease-like domain and displays structural similarity to LegA3/AnkD, but differs in host cell localization

Legionella pneumophila protein effector LegA15/AnkD contains an ankyrin-repeat domain, a cysteine protease-like domain with His268–Asn290–Cys361 putative catalytic triad, and a helix-bundle domain. LegA15/AnkD shows structural similarity to another effector, LegA3/AnkH, but they localize to different cellular compartment within the host.

Helical filament structure of the DREP3 CIDE domain reveals a unified mechanism of CIDE-domain assembly

The CIDE domain was initially identified in apoptotic nucleases and now forms a highly conserved family with diverse functions ranging from cell death to lipid metabolism. Based on structural determination of the DREP3 domain, it is suggested that the head-to-tail helical filament structure might be a unified mechanism of CIDE-domain assembly and represents a critical higher-order scaffolding structure that is important for the function of CIDE-domain-containing proteins in DNA fragmentation and lipid-droplet fusion.

Structural and biochemical analyses of the tetrameric carboxypeptidase S9Cfn from Fusobacterium nucleatum

Extensive biochemical assays revealed that a putative peptidase S9Cfn from Fusobacterium nucleatum is a carboxypeptidase rather than an aminopeptidase as previously noted. Combined with the 2.6 Å tetramer structure of S9Cfn, key residues for substrate binding and catalysis, as well as the underlying mechanism of the catalytic cycle was revealed for S9C peptidase family.

Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions

The X-ray structure of BbgIII, a multidomain β-galactosidase from B. bifidum, determined using an intact protein corresponding to a gene construct of eight domains is reported.

The impact of folding modes and deuteration on the atomic resolution structure of hen egg-white lysozyme

A study of in vitro refolding and isotope effects on protein structure, activity and stability shows that different folding dynamics can lead to important changes in protein properties.

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.

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.

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.