Advances in membrane protein crystallography: in situ and in meso data collection

Membrane protein structural biology has made tremendous advances over the last decade but there are still many challenges associated with crystallization, data collection and structure determination. Two independent groups, Axford et al. [(2015), Acta Cryst. D71, 1228–1237] and Huang et al. [(2015), Acta Cryst. D71, 1238–1256], have published methods that make a major contribution to addressing these challenges.

Structure determination of an integral membrane protein at room temperature from crystals in situ

The X-ray structure determination of an integral membrane protein using synchrotron diffraction data measured in situ at room temperature is demonstrated.

In meso in situ serial X-ray crystallography of soluble and membrane proteins

A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing.

The structure of the giant haemoglobin from Glossoscolex paulistus

The structure of the giant haemoglobin from G. paulistus was determined.

Bond distances in polypeptide backbones depend on the local conformation

Statistical surveys of protein structures combined with quantum-mechanical calculations reveal a systematic dependence of bond distances on conformation. Interestingly, the variability of backbone C—O and C—N distances is not directly related to peptide-bond planarity.

Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe

The crystal structure of fission yeast Dis3l2 displays an open conformation that differs from that in the mouse Dis3l2–RNA complex.

The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket

S. aureus steals iron in the form of haem from human haemoglobin (Hb). The crystal structure of the S. aureus Hb receptor IsdH in complex with Hb shows that the receptor induces a conformational change in the globin haem pocket that may promote haem transfer.

The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C₂-symmetric hexamer

The hexameric structure of truncated A. aeolicus FtsH shows a molecular architecture that forms two rings, in which the ATPase ring possesses twofold symmetry and the protease ring possesses sixfold symmetry. The importance of a dynamic β-strand in the active site and a conserved glycine in the linker region is demonstrated in the full-length protein by site-directed mutagenesis.

Two crystal structures of the FK506-binding domain of Plasmodium falciparum FKBP35 in complex with rapamycin at high resolution

Reported here are two crystallographic structures of rapamycin in complex with the FK506-binding domain of Plasmodium falciparum PfFKBP35 at high resolution, in both its oxidized and reduced forms.

Structure of the bovine COPI δ subunit μ homology domain at 2.15 Å resolution

The crystal structure of the μ homology domain of the δ subunit of the bovine COPI complex was determined to 2.15 Å resolution. The structure reveals important aspects of interdomain flexibility that relate to the function of COPI.

Structural bases for N-glycan processing by mannoside phosphorylase

Crystal structures of the GH130 enzyme Uhgb_MP in the apo form and in complex with mannose and N-acetylglucosamine are described and the structural determinants of the functional specificities of the enzymes involved in N-glycan breakdown by human gut bacteria are identified.

DATASW, a tool for HPLC–SAXS data analysis

DATASW, a novel tool for the rapid processing of HPLC–SAXS data, is described.

Structural characterization of a novel subfamily of leucine-rich repeat proteins from the human pathogen Leptospira interrogans

The crystal structures of four representative LRR proteins from the pathogen Leptospira interrogans have been solved, providing insights into a novel subfamily of bacterial LRR characterized by consecutive stretches of a 23 amino-acid repeat motif.

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7^T: crystal structure and function of a desulfinase with an acyl-CoA de­hydrogenase fold

3-Sulfinopropionyl-coenzyme A desulfinase (Acd_DPN7) is a novel desulfinase which catalyzes sulfur abstraction in the catabolic pathway of 3,3′-dithiodipropionic acid. The crystal structures of native Acd_DPN7 at 1.89 Å resolution and of native Acd_DPN7 soaked with the substrate analogue succinyl-CoA at 2.30 Å resolution revealed an acyl-CoA dehydrogenase fold with Arg84 as a key residue in the desulfination reaction.

Full-length structure of the major autolysin LytA

The full-length structure of the major autolysin LytA from S. pneumoniae combined with enzymatic activity assays suggest that dimerization and full occupancy of all choline-binding sites are indispensable for the full activity of LytA in vivo.

Structural analysis of the α-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism

The structures of complexes of HaG and its mutants revealed the substrate specificity and catalytic mechanism of HaG.

Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis

The PPM II phosphatase RsbX features a catalytic centre that binds two Mn²⁺ ions using five residues instead of the usual four as in PPM I phosphatases, with a conformational reorganization that tilts a flexible loop towards the second Mn²⁺ ion for coordination of the fifth residue.

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å.