issue contents

Journal logoSTRUCTURAL
ISSN: 2059-7983

December 2021 issue

Highlighted illustration

Cover illustration: The validation of automatically generated stereochemical restraints highlights the limitations of using such restraints and the fragility of creating ideal geometry – one of the things Roversi & Tronrud `hate' about refinement [Roversi & Tronrud (2021), Acta Cryst. D77, 1497–1515].



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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.

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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.

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

research papers

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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.

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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.

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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.

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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.

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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.

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

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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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