Structural biology of coronavirus ion channels

Knowledge of the structure and function of ion-channel proteins coded by coronaviruses lags behind the enormous progress on the other proteins of the SARS-CoV-2 virus, the etiological agent of COVID-19. The disease increasingly appears to constitute a complex syndrome of systemic breadth, making viral ion-channel proteins a possible target for therapeutic interventions.

Using RELION software within the Scipion framework

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

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, experiences in preparing kinesin-binding protein (KBP; 72 kDa) and KBP–kinesin motor domain (110 kDa) samples for cryo-EM are detailed, in particular some of the challenges and opportunities arising from surface interactions on the cryo-EM grid.

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.

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.

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.

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.

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.

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.

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.

The structure of Prp2 bound to RNA and ADP-BeF₃⁻ reveals structural features important for RNA unwinding by DEAH-box ATPases

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.

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

Biotin protein ligase from Leishmania major in complex with biotinyl-5′-AMP or biotin, crystallizes as a unique dimer, formed by cross-handshake interactions of its C-terminal domain.

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.

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

Cryo-EM can produce maps with resolutions that are sufficiently high that fine structural details can be discerned. Using calculated electrostatic potential maps, it is shown 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.

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.