New tools for the analysis and validation of cryo-EM maps and atomic models

New methods and PHENIX tools for quality assessment of cryo-EM maps, atomic models and model-to-map fitting are presented. Results of systematic application of these tools to high-resolution cryo-EM maps and corresponding atomic models are analyzed and discussed.

Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 Å resolution

The complete post-fusion core structure of the Human coronavirus 229E spike protein was determined at 1.86 Å resolution. Comparison of the interactions between heptad repeats HR1 and HR2 in different human coronaviruses reveals some differences, which should be taken into consideration when designing pan-coronavirus HR2-mimicking inhibitors that target HR1.

Crystal structure of the Acinetobacter baumannii outer membrane protein Omp33

The X-ray crystal structure of Omp33 is reported at a resolution of 2.1 Å. The structure helps in understanding how Acinetobacter baumannii outer membrane proteins contribute to the low permeability of the cell envelope and suggests that Omp33 may function as a ligand-gated channel.

Structure and function of L-threonine-3-de­hydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations

Relationships between the structure and function of a putative drug target for human African trypanosomiasis have been elucidated using X-ray crystallography and geometric simulations. The data presented provide insights into ligand binding and catalysis, giving direction to future rational drug design.

Improving signal strength in serial crystallography with DIALS geometry refinement

For XFEL data, simultaneous refinement of multi-panel detector geometry with thousands of crystal models in the program DIALS improves the integrated signal quality and helps to reduce non-isomorphism

High-pressure protein crystal structure analysis of Escherichia coli di­hydrofolate reductase complexed with folate and NADP⁺

High-pressure crystal structure analysis of E. coli dihydrofolate reductase (ecDHFR) complexed with folate and NADP⁺ was performed up to 800 MPa. A pressure-induced phase transition of monoclinic ecDHFR crystals and structural changes closely related to its reaction mechanism were observed.

The crystal structure of an essential high-temperature requirement protein HtrA1 (Rv1223) from Mycobacterium tuberculosis reveals its unique features

High-temperature requirement A (HtrA) proteins belong to the serine protease family and possess protease and PDZ domains. HtrA1 is an essential membrane protein in Mycobacterium tuberculosis.

The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order

Cryosolution thermal contraction is found to have an impact on cryocooled protein and unit-cell volumes and conformations. In some cases, its adjustment can produce higher quality diffraction data.

Crystallographically correct but confusing presentation of structural models deposited in the Protein Data Bank

Attention is brought to the fact that many coordinate sets deposited in the Protein Data Bank are located outside of the unit cells and are sometimes presented in space groups with symmetry lower than the true space group, and that symmetric oligomers are sometimes scattered, making it harder for the users to interpret quaternary structures.