Structure of the mexicain–E-64 complex and comparison with other cysteine proteases of the papain family

A comparison of the binding site of mexicain for E-64 with those of other E-64–cysteine protease complexes shows that highly conserved interactions are replaced by other interactions in which water molecules play an essential role.

Heterogeneous nucleation of three-dimensional protein nanocrystals

Human hair was identified to be a versatile nucleant surface and was applied successfully for the crystallization of various proteins. Despite the rather complex mechanism of heterogeneous crystallization, it was discovered that the surface properties and the chemical composition together define the nucleation properties of the selected surface.

Structures of vaccinia virus dUTPase and its nucleotide complexes

The vaccinia virus dUTPase structure shows an increased size of the central channel within the homotrimer.

Structure of the equine arteritis virus nucleocapsid protein reveals a dimer–dimer arrangement

Arteriviruses form a family of enveloped, positive-sense RNA viruses that includes important agricultural pathogens such as EAV. The EAV nucleocapsid protein forms an arrangement of dimers in the crystal structure that may reflect its organization in the virus.

Structure of a CBS-domain pair from the regulatory γ1 subunit of human AMPK in complex with AMP and ZMP

The structure of a CBS-domain pair from human AMPK γ1 in complex with the physiological activator AMP and the pharmacological activator ZMP (AICAR) is presented.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal.

Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?

An evaluation of the geometrical restraints used in the refinement of protein structures is presented based on currently available protein and small-molecule structural databases.

Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions

The human formylglycine-generating enzyme was cocrystallized with bromide and iodide ions, which, among other positions, occupy an oxygen-binding pocket that is crucial for enzyme catalysis. Halide ions may substitute for xenon in the detection of oxygen-binding sites.

A Rac1–GDP trimer complex binds zinc with tetrahedral and octahedral coordination, displacing magnesium

The crystal structure of a Rac1–GDP–Zn complex shows that Rac1 can coordinate zinc in a tetrahedral fashion by using residues in its biologically relevant switch I and switch II structural regions. Additionally, zinc can replace the normally coordinated magnesium without the perturbation of GDP from the small GTPase.

Protein crystallization by surface entropy reduction: optimization of the SER strategy

A systematic study of the effect of substituting five different residues for large, solvent-exposed and flexible amino acids has been conducted using traditional and alternate reservoir screens. The results suggest a strategy that may enhance the success rates of preparation of X-ray quality crystals of proteins that are otherwise recalcitrant to crystallization in their wild-type form.

Crystallization by capillary counter-diffusion and structure determination of the N114A mutant of the SH3 domain of Abl tyrosine kinase complexed with a high-affinity peptide ligand

The crystallographic structure of the N114A mutant of the SH3 domain of the Abelson leukaemia virus tyrosine kinase complexed with a high-affinity peptide is reported. An X-ray diffraction data set was collected directly from crystals from the initial screening using the capillary counter-diffusion technique.

High-pressure cryocooling for capillary sample cryoprotection and diffraction phasing at long wavelengths

It is shown that a high-pressure cryocooling method enables the phasing of macromolecular structures using either Xe or native S atoms. The method may even be used for crystals in capillaries.

Notes of a protein crystallographer: quo vadis structural biology?

The origins of molecular and structural biology are briefly discussed in the context of the current status of the field. The future of structure biology is reviewed suggesting that in order to reach a new level of understanding of biological processes is necessary to include the notions of dissipative structures within the conceptual framework of non-equilibrium thermodynamics.