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 3 March 2021

Intermediates in allosteric equilibria of DnaK–ATP interactions with substrate peptides

ATP and client peptides interact allosterically to effect molecular chaperone activity by which Hsp70 proteins promote protein folding. Here, we describe two structures of DnaK-ATP, one with implications for a transition by which peptides are released upon the binding of ATP and one with relevance for the rebinding and capture of client polypeptides.

Accepted 2 March 2021

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

A data processing pipeline to solve structures from tomograms of protein nanocrystals is presented and validated using simulated crystals. The robustness of this workflow to radiation damage is assessed to investigate optimal data collection strategies.

Accepted 27 February 2021

PCA is limited to low-resolution analysis in CryoEM

Accepted 24 February 2021

Crystal structures of UDP-N-acetylmuramic acid l-alanine ligase (MurC) from Mycobacterium bovis with and without UDP-N-acetylglucosamine

MbMurC binds UNAG, MurA's substrate, and its complex crystal structure was determined.

Accepted 23 February 2021

Coma-corrected rapid single-particle cryo-EM data collection on the cryoARM300

Accepted 17 February 2021

Cryo-EM of kinesin-binding protein: challenges and opportunities from protein-surface interactions

Sample preparation is a major limiting factor in cryo-electron microscopy (cryo-EM), particularly for small macromolecules under 100 kDa. Here we detail our experiences preparing KBP (72 kDa) and KBP-kinesin motor domain (110 kDa) samples for cryo-EM and in particular some of the challenges and opportunities arising from surface interactions on the cryo-EM grid.

Accepted 17 February 2021

Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate the distinct metal-dependent activity with a crucial residue for catalysis

Crystal structures of SAV1707apo and SAV1707cAMP-bound, UPF0173 metal-dependent hydrolase family from Staphylococcus aureus were determined at 2.05 Å and 1.55 Å resolutions providing functional and structural insights into the catalytic mechanism of SAV1707.

Accepted 16 February 2021

Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps

Cryo-EM can produce maps with resolutions so high that fine structural details can be discerned. Using calculated electrostatic potential maps we show that it is possible to identify Mg2+ ions bound to nucleotide bases at which no charge compensation occurs, in contrast to Mg2+-bound phosphate groups in the ribosomal RNA.

Accepted 15 February 2021

Integrated sample handling and mounting system for fixed-target serial synchrotron crystallography

A highly flexible, integrated system for preparing samples for serial synchrotron crystallography at room and cryogenic temperatures is described and evaluated. The system is compatible with existing infrastructure for high-throughput crystallography at synchrotrons and addresses major issues in maximizing data quantity and quality from large numbers of small crystals.

Accepted 15 February 2021

Using RELION software within the Scipion framework

An overview of the Scipion plugin for the Relion software package is presented and various capabilities of image processing within the Scipion framework are discussed.

Accepted 14 February 2021

Control of strains in subgrains of protein crystals by introduction of grown-in dislocations

It is demonstrated that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality was rather high, as showed by clear equal-thickness fringes in X-ray topography. By controlling the local strains in subgrains, the resistance of subgrains of protein crystals to radiation damage could be improved, enabling the collection of XRD data sets with high diffractivity.

Accepted 12 February 2021

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

A procedure for the identification of a protein in a map from electron cryomicroscopy based on automated model building and sequence assignment is presented.

Accepted 12 February 2021

Modelling covalent linkages in CCP4

The mechanism for modelling covalent linkages in CCP4 is reviewed and the method of link-dictionary generation used by AceDRG is described. An overview of the various protocols available for the modelling and application of covalent linkages within the CCP4 suite is presented, providing instructive guidelines with a focus on practical application.

Accepted 9 February 2021

Structure of the class XI myosin globular tail reveals evolutionary hallmarks for cargo recognition in plants

This study reveals the first crystal structure of a myosin XI globular tail domain and highlights the molecular adaptations that have allowed the evolution of specific mechanisms for the intracellular transport of vesicles and organelles in plant cells.

Accepted 8 February 2021

Leishmania major biotin protein ligase forms as a unique cross-handshake dimer

Accepted 2 February 2021

The structure of Prp2 bound to RNA and ADP-BeF3 reveals structural features important for RNA unwinding

The crystal structure of Chaetomium thermophilum Prp2 bound to ADP-BeF3 and a poly-U12 RNA reveals a conserved pre-catalytic helicase conformation and only minor shifts of the C-terminal domains. Differences in the hook-loop and a loop of the helix-bundle domain compared with Prp43 evoke divergent conformations of the bound RNA, ultimately impacting the ability to unwind double-stranded RNA.

Accepted 2 February 2021

Theoretical and practical approaches to improve the performance of local correlation algorithms for volume data analysis and shape recognition

Several approaches are presented to improve the performance of local correlation algorithms based on prior information about 3D search and target maps.

Accepted 2 February 2021

Crystal structures of β-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies

Crystal structures of human β-1,4-N-acetylglucosaminyltransferase 2, an enzyme essential for O-mannosylation, are reported, revealing a novel domain organization and providing the first rational basis for an explanation of the loss-of-function mutations observed in the clinic.

Accepted 1 February 2021

Adaptive Cartesian and torsional restraints for interactive model rebuilding

New forms of adaptive or top-out distance and torsion restraints are described that are suitable for restraining a model to match a reference structure during interactive rebuilding. In addition, their implementation in ISOLDE is described, along with some illustrative example applications.

Accepted 1 February 2021

Ice in biomolecular cryocrystallography

Analysis of diffraction data from three proteins indicates that the ice formed in internal crystal solvent is stacking-disordered. Application of a revised metric and algorithm for detecting ice from protein structure-factor data indicates that roughly 3.9% of PDB entries exhibit ice that is primarily hexagonal and 11.7% exhibit stacking-disordered ice.

Accepted 29 January 2021

Guest-protein incorporation into solvent channels of a protein host crystal (hostal)

This study reports the incorporation of small guest proteins by diffusion (soaking) into the solvent channels of a host protein crystal, visualized in time and space by microscopic techniques. The results represent a first step towards the realization of a protein-based crystal host (`hostal') system that may be used in the future as a carrier/entrainment system for protein guests and/or for guest-protein structure determination.

Accepted 24 January 2021

Vagabond: bond-based parametrization reduces overfitting for refinement of proteins

Reparametrizing the positions and flexibility of protein models for refinement against diffraction data results in a substantial reduction in the number of parameters. This produces maps that are less affected by model bias, which allow the maps to more faithfully reflect the true crystal contents and reveal more biological information.

Accepted 4 January 2021

Depth-of-field extension in optical imaging for rapid crystal screening

The addition of a single optical element enabled a 2.8-fold reduction of the data-acquisition time in crystal-screening processes based on optical imaging approaches.

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