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 21 March 2017

Free Radicals in Biology and Medicine. Fifth Edition. By Barry Halliwell and John M. C. Gutteridge. Oxford University Press, 2015. Pp. xxxviii + 905. Price GBP 70.00 (paperback, ISBN 9780198717485), GBP 125.00 (hardback, ISBN 9780198717478).

The fifth edition of Free Radicals in Biology and Medicine by Barry Halliwell and John M. C. Gutteridge is reviewed.

Accepted 21 March 2017

Biotechnology. Edited by Ulrich Kück and Nicole Frankenberg-Dinkel. De Gruyter, 2015. Pp. XV+443. Price 49,95 EUR/70.00 USD/37.99 GBP (Paperback). ISBN 978-3-11-034110-2.

A review of the book Biotechnology. Edited by Ulrich Kück and Nicole Frankenberg-Dinkel.

Accepted 21 March 2017

Metallomics. A Primer of Integrated Biometal Sciences. By Wolfgang Maret. Imperial College Press, 2016. Pp. xiii + 141. Price GBP 30.00 (paperback, ISBN 978-1-78326-828-3), GBP 56.00 (hardback, ISBN 978-1-78326-827-6).

Metallomics. A Primer of Integrated Biometal Sciences by Wolfgang Maret is reviewed.

Accepted 20 March 2017

Cryo-electron microscopy of chromatin biology

This review article summarizes recent progress in our understanding of chromatin biology based on single-particle cryo-electron microscopy studies.

Accepted 14 March 2017

The first plant acyl-CoA-binding protein structures determined from two close homologues in rice

The first structures of plant acyl-CoA-binding proteins elucidated from rice show similarity to the human liver and bovine homologues.

Accepted 14 March 2017

Trends in EMDB

The Electron Microscopy Data Bank (EMDB) – the public archive for three-dimensional EM reconstructions is an invaluable resource for obtaining a birds-eye view of trends affecting the cryo-EM field. EMDB is growing rapidly with almost a quarter of the entries having been released over the past year.

Accepted 14 March 2017

Responses to `Atomic resolution': a badly abused term in structural biology

Accepted 13 March 2017

The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design

Recent developments in electron microscopy have provided new opportunities in the structure based drug design field. This review looks at the challenges that remain and future prospects for the use of electron microscopy in this area.

Accepted 13 March 2017

Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis

The structure of the family B DNA polymerase from the hyperthermophilic archaeon P. calidifontis has been determined with an R factor of 24.47% and an Rfree of 28.81% at 2.80 Å resolution. The enzyme has a number of unique structural features which distinguish it from other archaeal DNA polymerases.

Accepted 9 March 2017

Structural features of NS3 of Dengue virus serotypes 2 and 4 in solution and insight into RNA binding and the inhibitory role of quercetin

The NS3s of Dengue virus serotypes 2 and 4 are elongated and dynamic in solution. The protease domain of NS3 undergoes substantial conformational alterations owing to RNA binding. The interactions and effects of quercetin binding in NS3 are described.

Accepted 7 March 2017

Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water by Steccherinum murashkinskyi laccase: insights into the reaction mechanism

A series of diffraction data sets with increasing absorbed radiation dose were collected from one crystal of S. murashkinskyi laccase at 1.35 Å resolution. The mechanism of oxygen reduction catalyzed by laccases is discussed.

Accepted 28 February 2017

The Dynamo package for tomography and subtomogram averaging: components for Matlab, GPU computing and EC2 Amazon Web Services

A technical description of the Dynamo software package for subtomogram averaging is provided. Details are given on advanced Matlab libraries, parallelization strategies, the use of GPU and accessibility though the Amazon cloud computing services.

Accepted 22 February 2017

Low-dose fixed-target serial synchrotron crystallography

A time- and sample-efficient approach for the serial collection of room-temperature diffraction data using a fixed target at a synchrotron is demonstrated.

Accepted 16 February 2017

Crystal structures of Hsp104 N-terminal domains from Saccharomyces cerevisiae and Candida albicans suggest the mechanism for the function of Hsp104 in dissolving prions

The crystal structures of Hsp104 N-terminal domains from S. cerevisiae (ScHsp104NTD) and C. albicans (CaHsp104NTD) were determined to high resolution. The structures of ScHsp104NTD and CaHsp104NTD reveal that the yeast Hsp104 N-terminal domain may utilize a conserved putative peptide-binding groove to interact with misfolded polypeptides.

Accepted 14 February 2017

Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association

In eight of the nine crystal structures of M. smegmatis MutT1 reported here, an arrangement is observed in which domain 1 of one molecule and domain 2 of a neighbouring molecule (trans domain 2) are brought into close proximity, with ligand-binding sites at the interface between the two domains. This and other structural observations, along with biochemical results, lead to a plausible proposal for the mechanism of action of the enzyme.

Accepted 9 February 2017

1.8 Å resolution crystal structure of the carbapenem intrinsic resistance protein CarF

The crystal structure of the carbapenem-resistance protein CarF has been determined at 1.8 Å resolution. CarF confers partial intrinsic resistance to the naturally occurring antibiotic 1-carbapen-2-em-3-carboxylic acid.

Accepted 9 February 2017

`Atomic resolution': a badly abused term in structural biology

The term `atomic resolution' is very often abused in presenting macromolecular structures.

Accepted 8 February 2017

Is dimerization a common feature in thioredoxins?: the case of thioredoxin from Litopenaeus vannamei

This study of shrimp thioredoxin sheds new light on the existence of monomeric and dimeric populations in solution. It is demonstrated that the Cys73 residue is essential for dimer formation and that the Cys73Ser mutant has the same activity as the wild type.

Accepted 8 February 2017

Crystal structures of human 3-hydroxyanthranilate 3,4-dioxygenase with native and non-native metals bound in the active site

Two structures of human 3-hydroxyanthranilate 3,4-dioxygenase, one with iron bound at the active site and one with zinc bound at the active site, are reported.

Accepted 13 January 2017

Dissecting random and systematic differences between noisy composite data sets

A multidimensional scaling analysis of pairwise correlation coefficients is presented which positions data sets in a sphere with unit radius of an abstract, low-dimensional space at radii inversely proportional to their levels of random error and at spherical angles related to their mutual systematic differences. This reduction in dimensionality can not only be used for classification purposes, but also to derive data-set relations on a continuous scale.

Accepted 12 January 2017

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Using all available metal-containing organic compound structures in the Cambridge Structural Database, a novel data-driven method to derive bond-valence R0 parameters was developed. While confirming almost all reference literature values, we observe two distinct populations of FeII—N and FeIII—N bonds, which are interpreted as low-spin and high-spin states of the coordinating iron. Based on the R0 parameters derived here, guidelines for the modeling of iron–ligand distances in macromolecular structures are suggested.

Accepted 2 January 2017

Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

The structure of an Hfq homolog from the deep-branching thermophilic bacterium A. aeolicus, determined to 1.5 Å resolution both in the apo form and bound to a uridine-rich RNA, reveals a conserved, pre-organized RNA-binding pocket on the lateral rim of the Hfq hexamer.

Accepted 2 December 2016

A pipeline approach to single-particle processing in RELION

The formal description of a workflow to cryo-EM structure determination in the RELION program allows standardization of procedures and on-the-fly image processing during data acquisition.

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