Decision making in macromolecular crystallography: how to be a productive structural biologist

The Guest Editors introduce the special issue based on talks at the CCP4 Study Weekend 2024. The virtual issue is available at https://journals.iucr.org/special_issues/2026/CCP42024/.

Avoiding pitfalls when modelling ligands in macromolecular crystallography

Flawed protein–ligand X-ray structures can misdirect drug discovery based on PDB-deposited models. This review uses publicly available PDB examples to highlight potential pitfalls, from absent ligands to incorrect chemistry, and presents a practical validation approach to improve model reliability.

Structure and allostery in major facilitator superfamily symport mechanisms

Conformational dynamics in the melibiose/Na⁺ cotransporter MelB significantly influence the binding of the primary sugar substrate but have minimal effect on the co-substrate Na⁺. Na⁺ acts as an allosteric activator, increasing sugar affinity by stabilizing the inner barrier and constraining conformational flexibility.

Towards routine accurate electron-density studies of biological macromolecules

Here, we describe the determination of the highest resolution structure in the PDB at 0.43 Å resolution. Electron-density maps reveal extensive deformation electron density that is completely accounted for by performing transferable aspherical atom refinements using the DiSCaMB library in BUSTER.

Direct deposition on pre-cooled grids: a new approach to sub-millisecond cryoEM grid preparation

We describe a new method to prepare grids for cryoEM on the sub-millisecond timescale.

Influence of heme and pH on the oligomeric states of Brucella melitensis bacterioferritin

The oligomerization of B. melitensis bacterioferritin (BmBfr) was studied using X-ray crystallography, size-exclusion chromatography and thermal shift analysis. These techniques allowed the characterization of both apo and holo BmBfr, highlighting the impact of heme and pH on the oligomerization mechanism.

Room-temperature crystal structure of a metal-dependent W-formate de­hydrogenase by serial synchrotron crystallography

We report a room-temperature serial synchrotron X-ray crystallographic structural analysis of Nitratidesulfovibrio vulgaris formate dehydrogenase AB, an enzyme that reduces CO₂ to formate.

Structural basis for T-cell receptor recognition of p53^Y220D, a human cancer neo­antigen

We determined crystal structures of TCR 4414A bound to HLA-A2-presented p53^Y220D and of the corresponding unbound wild-type and mutant p53–HLA-A2 ligands, revealing that the Y220D driver mutation reshapes the peptide and renders a normally cryptic self-epitope visible to T cells. These structures explain how TCR 4414A achieves high specificity for mutant p53 by minimizing interactions with conserved peptide regions and instead focusing on the central Y220D mutation, providing a structural basis for mutation-specific TCR immunotherapy.

QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning

QwenCryoMarker is a universal post-processing framework that removes contamination-induced false positives from any cryo-EM particle picker. Built on the Qwen-Image-Edit vision-language model, it generates high-precision masks of carbon, ice and impurities, and then filters raw particle coordinates with negligible loss of true particles.

KAT6A–inhibitor co-crystal structures: tackling a challenging crystallization target via two alternative approaches

We report a novel cysteine-to-serine surface-mutation approach to determine co-crystal structures of KAT6A with small-molecule inhibitors and compare it with the previously published MYST^cryst approach which uses mutated KAT8 as a surrogate for KAT6A. A series of co-crystal structures obtained from both approaches, with three different inhibitor chemotypes, reveal alternative inhibitor conformations at the binding-site entry and the importance of filling a hydrophobic subpocket. These insights expand the experimental basis for future KAT6A inhibitor design for cancer therapy.