forthcoming articles in Acta Crystallographica Section D

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

See also Forthcoming articles in all IUCr journals.

Accepted 31 July 2015

Structural and functional evidence for membrane docking and disruption sites on phospholipases A2-like proteins revealed by complexation with suramin inhibitor

G. H. M. Salvador, T. R. Dreyer, W. L. G. Cavalcante, F. F. Matioli, J. I. dos Santos, A. Velazquez-Campoy, M. Gallacci and M. R. M. Fontes

Synopsis: in vitro neuromuscular studies were performed to demonstrate that suramin neutralizes toxic activity of a PLA2-like proteins corroborating with calorimetric assays. Crystallographic studies demonstrated that the inhibitor binds to the surface of the toxin, obstructing its membrane docking and disruption sites confirming the proposed myotoxic mechanism.

Accepted 29 July 2015

Response from J R Helliwell et al to Shabalin et al (2015)

S. W. M. Tanley, K. Diederichs, L. M. J. Kroon- Batenburg, C. Levy, A. M. M. Schreurs and J. R. Helliwell

Synopsis: Response from J R Helliwell et al to Shabalin et al (2015)

Accepted 29 July 2015

Response to "Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin," by Shabalin et al.

A. K. Boal and A. C. Rosenzweig

Synopsis: Response to Shabalin et al.

Accepted 27 July 2015

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA

H. L. Pedersen, K. A. Johnson, C. E. McVey, I. Leiros and E. Moe

Synopsis: The high resolution structure of uracil-DNA N-glycosylase (UNG) from D. radiodurans in complex with DNA provides support for a model where DNA compression and minor groove stabilization is crucial for the uracil damage detection mechanism of UNGs.

Accepted 27 July 2015

In vacuo X-ray data collection from graphene-wrapped protein crystals

A. J. Warren, A. D. Crawshaw, J. Trincao, P. Aller, S. Alcock, I. Nistea, P. S. Salgado and G. Evans

Synopsis: A method is reported for collecting room temperature data from protein crystals under vacuum by protecting them with a thin graphene layer.

Accepted 22 July 2015

The novel double-folded structure of d(GCATGCATGC) - a possible model for triplet repeat sequences

A. Thirugnanasambandam, S. Karthik, P. K. Mandal and N. Gautham

Synopsis: The self-complementary DNA decamer d(GCATGCATGC) crystallizes as an unusual double-folded structure, which serves as the basis for a possible structural model of triplet repeat DNA sequences.

Accepted 22 July 2015

Complete epitopes for vaccine design derived from a crystal structure of broadly neutralizing antibodies PGT128 and 8 ANC195 in complex with an HIV-1 Env trimer

L. Kong, A. Torrents de la Peña, M. C. Deller, F. Garces, K. Sliepen, Y. Hua, R. L. Stanfield, R. W. Sanders and I. A. Wilson

Synopsis: The crystal structure of broadly neutralizing antibodies 8 ANC195 and PGT128 bound to an HIV-1 envelope trimer has been determined. Structural and binding analyses have elucidated the full epitopes for these antibodies in the context of the intact viral glycoprotein, providing improved templates for HIV-1 vaccine design.

Accepted 22 July 2015

Comparison of Epsilon- and Delta-Class Gluta­thione S-transferases: The Crystal Structures of Gluta­thione S-transferase-E6 and E7 from Drosophila melanogaster

M. Scian, I. Le Trong, A. M. A. Mazari, B. Mannervik, W. M. Atkins and R. E. Stenkamp

Synopsis: Epsilon class glutathione S-transferases (GSTs) are found in invertebrates, including many insects, where they play roles in detoxication of insecticides and development. The crystal structures of two epsilon class GSTs from Drosophila melanogaster are reported and compared to aid in characterization of functional differences between the isozymes.

Accepted 22 July 2015

Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease

M. Li, A. Gustchina, R. Cruz, M. Simões, P. Curto, J. Martinez, C. Faro, I. Simões and A. Wlodawer

Synopsis: Crystal structures of two constructs of RC1339/APRc from Rickettsia conorii, consisting of either residues 105-231 or 110-231 followed by a His tag, have been determined in three different crystal forms. The monomer of APRc assumes retropepsin-like fold, but the dimer observed in all crystal forms is entirely different from the canonical dimer of retropepsins.

Accepted 21 July 2015

Structural basis for amino acid recognition and transmembrane signaling by tandem-Per-Arnt-Sim (tandem-PAS) chemoreceptor sensory domains

Y. C. Liu, M. P. Machuca, S. A. Beckham, M. J. Gunzburg and A. Roujeinikova

Synopsis: A structural insight is provided into the mechanism of how a widespread family of bacterial chemotaxis receptors containing the periplasmic tandem-Per-Arnt-Sim (PAS) sensing domain recognize free amino acids, and a model for signal transduction across the membrane is proposed.

Accepted 20 July 2015

Structural basis for the sequestration of the anti-[sigma]70 factor Rsd from [sigma]70 by the histidine-containing phosphocarrier protein HPr

Y.-H. Park, S.-H. Um, S. Song, Y.-J. Seok and N.-C. Ha

Synopsis: The crystal structure of an Rsd-HPr complex was determined in order to reveal the binding interface between Rsd and HPr. A molecular link between global gene regulation and nutrient availability is described.

Accepted 20 July 2015

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase

M. Alahuhta, L. E. Taylor, R. Brunecky, D. W. Sammond, W. Michener, M. W. W. Adams, M. E. Himmel, Y. J. Bomble and V. Lunin

Synopsis: The catalytic mechanism and low pH optimum of C. bescii family 3 pectate lyase are explained.

Accepted 9 July 2015

A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

R. J. Read and A. J. McCoy

Synopsis: A new Rice function approximation for the effect of intensity measurement errors improves the treatment of weak intensity data in calculating log-likelihood-gain scores in crystallographic applications including experimental phasing, molecular replacement and refinement.

Accepted 8 July 2015

Combining phase information in reciprocal space for molecular replacement with partial models

C. Millán, M. Sammito, I. Garcia-Ferrer, T. Goulas, G. M. Sheldrick and I. Usón

Synopsis: ARCIMBOLDO solves the phase problem starting from small model fragments placed in the asymmetric unit. Density modification aids in combining phase information from correct solutions to avoid a combinatorial explosion of sequential searches.

Accepted 7 July 2015

Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase

Y. Amano, I. Namatame, Y. Tateishi, K. Honboh, E. Tanabe, T. Niimi and H. Sakashita

Synopsis: X-ray structural analysis of T. cruzi spermidine synthase was conducted to identify novel inhibitor-binding sites, including an allosteric site, and to elucidate inhibition mechanisms.

Accepted 7 July 2015

Crystallographic studies of two variants of Pseudomonas aeruginosa IMPDH with impaired allosteric regulation

G. Labesse, T. Alexandre, M. Gelin, A. Haouz and H. Munier-Lehmann

Synopsis: High-resolution structures of a variant of an IMPDH enzyme with the regulatory CBS motifs deleted, as well as a point-mutation variant, have been solved and provide new insights into the allosteric behaviour and the octameric structure of the enzyme.

Accepted 7 July 2015

Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-de­methylase shed light on methyltetra­hydro­folate formation

H. Sjuts, M. S. Dunstan, K. Fisher and D. Leys

Synopsis: The first crystal structures of an O-demethylase methyltransferase protein in apo, THF-bound and MTHF-bound forms are reported. A conserved asparagine residue position is altered in favour of a putative proton-relay network.

Accepted 7 July 2015

Iron binding to human heavy-chain ferritin

C. Pozzi, F. Di Pisa, C. Bernacchioni, S. Ciambellotti, P. Turano and S. Mangani

Synopsis: Time-lapse crystal structures of human H-chain ferritin loaded with iron show the distribution of the substrate metal ion within the catalytic site. Comparison of these data with previously determined X-ray structures of R. catesbeiana M ferritin points to a number of shared and unshared features of the active sites of the two proteins that contribute to the ongoing debate on the possible existence of a universal mechanism for iron oxidation in all ferritins.

Accepted 6 July 2015

Structural insights into conformational switching in the copper metalloregulator CsoR from Streptomyces lividans

T. V. Porto, M. A. Hough and J. A. R. Worrall

Synopsis: The structural changes associated with conformational switching in a copper-sensing metalloregulator are revealed. These highlight the importance of charge distribution in regulating DNA binding.

Accepted 6 July 2015

Refining a model electron-density map via the PhD method

M. C. Burla, B. Carrozzini, G. L. Cascarano, C. Giacovazzo and G. Polidori

Synopsis: The efficiency of the Phantom Derivative method, in its non ab initio variant, has been checked by using the phases obtained via molecular-replacement methods as a starting point.

Accepted 5 July 2015

Structure of the JmjC domain-containing protein NO66 complexed with Rpl8

C. Wang, Q. Zhang, T. Hang, Y. Tao, X. Ma, M. Wu, X. Zhang and J. Zang

Synopsis: The structure of the complex of NO66 and Rpl8 was solved in the native state and NO66 recognizes the consensus motif NHXH . Tetramerization is required for efficient substrate binding and catalysis by NO66.

Accepted 1 July 2015

Advances in molecular-replacement procedures: the REVAN pipeline

B. Carrozzini, G. L. Cascarano, C. Giacovazzo and A. Mazzone

Synopsis: The REVAN pipeline for automatic protein crystal structure solution via molecular replacement and density-guided optimization algorithms is described.

Accepted 30 June 2015

Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum

M.-K. Kim, J.-H. Kim, J.-S. Kim and S.-O. Kang

Synopsis: The crystal structure of the 34 kDa F-actin-bundling protein ABP34 from D. discoideum is reported.

Accepted 30 June 2015

An alternative RNA polymerase I structure reveals a dimer hinge

D. Kostrewa, C.-D. Kuhn, C. Engel and P. Cramer

Synopsis: The crystal structure of RNA polymerase I in an alternative crystal form at 5.5 Å resolution with three dimers in a pseudo-heptagonal helical arrangement is reported. The angle between the monomers in the three dimers differs markedly from that in previously reported high-resolution structures.

Accepted 23 June 2015

Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1

J. Park, A. M. Guggisberg, A. R. Odom and N. H. Tolia

Synopsis: Crystal structures of P. falciparum HAD1 in complex with three different substrates were solved in order to understand how cap-domain movement enables diverse substrate recognition by this sugar phosphatase.

Accepted 22 June 2015

Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein

Y. K. Mathiharan, H. S. Savithri and M. R. N. Murthy

Synopsis: Some interesting aspects of domain swapping, which is a unique method of protein oligomerization, are addressed, with the aim of understanding the role of interfaces and hinge regions in domain swapping.

Accepted 19 June 2015

Accounting for partiality in serial crystallography using ray-tracing principles

L. M. J. Kroon-Batenburg, A. M. M. Schreurs, R. B. G. Ravelli and P. Gros

Synopsis: Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data.

Accepted 9 June 2015

A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime

P. M. Legler, I. Soojhawon and C. B. Millard

Synopsis: Many small-molecule compounds have been shown to bind the peripheral anionic site (PAS) of acetylcholinesterase, but only a few have been shown by X-ray crystallography to induce specific structural changes in the enzyme. Here, an unexpected conformational change observed in the PAS upon the binding of an experimental bis-imidazolium oxime nerve-agent antidote is reported and the observed structures are correlated with measured binding and reactivation kinetics.

Accepted 4 June 2015

ARCIMBOLDO_LITE: single-workstation implementation and use

M. Sammito, C. Millán, D. Frieske, E. Rodríguez-Freire, R. J. Borges and I. Usón

Synopsis: ARCIMBOLDO solves the phase problem through massive combination of small fragments and density modification. The use and performance of the single-workstation implementation is described.

Accepted 27 May 2015

Data collection with a tailored X-ray beam size at 2.69 Å wavelength (4.6 keV): sulfur SAD phasing of Cdc23Nterm

M. Cianci, M. R. Groves, D. Barford and T. R. Schneider

Synopsis: Data collection with a tailored 50 µm diameter X-ray beam at 4.6 keV ([lambda] = 2.69 Å) at the newly established EMBL beamline P13 at PETRA III, allowed the crystal structure determination of the Cdc23Nterm homodimer (65.4 kDa, 12 Cys and 10 Met) by sulfur SAD phasing at 3.1 Å resolution while overcoming crystal twinning.

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