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MAP kinase complexed with two pyrrolotriazine-based inhibitors led to the elucidation of the high-affinity binding mode of these compounds.The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.
See also Forthcoming articles in all IUCr journals.
Synopsis: A pattern recognition-based method for identification of planar objects in crystallographic electron-density maps is presented. The accuracy of the located centres of the planes is of the order of 0.5 Å.
Synopsis: Improved classification of images from crystallization experiments is obtained using multiple classifiers to combine different feature-extraction methods.
Synopsis: The crystal structure of an NAD+-dependent quinate dehydrogenase from C. glutamicum has been solved. Enzymatic assays show that this enzyme belongs to a new functional class of bacterial shikimate/quinate dehydrogenases.
Synopsis: Separation of two individual lattices within an epitaxically twinned data set allowed the crystal structure of the V3-specific neutralizing antibody 447-52D in complex with a V3 peptide (UG1033) to be determined. The structure confirms that the neutralization breadth of 447-52D is likely to be attributable to the extensive focus on main-chain hydrogen-bond interactions with the peptide that permit recognition of a range of V3 sequences. Given the high similarity to previously reported V3-peptide structures, this further reinforces the notion that the key structural features of the HIV-1 V3 loop are highly conserved and in this case the two amino-acid differences do not introduce any changes to the conformation of the V3 loop that might alter its interaction with or specificity to the HIV-1 chemokine co-receptors such as CCR5 or CXCR4.
Synopsis: Crystal structures of urate oxidase from A. globiformis and its complexes with uric acid, allantoate and 8-azaxanthin demonstrate the details of substrate recognition and catalysis.
Synopsis: The three-dimensional structure of human pancreatic carboxypeptidase A1 reveals the mode of binding of a polymer with drug-protecting effects and is used to apply optimal docking area analysis to characterize binding sites for multiprotein complexes.
Synopsis: The high-resolution structure of HIV-1 subtype C protease contributes to the understanding of flap dynamics and drug resistance.
Synopsis: Backbone amide hydrogen/deuterium-exchange patterns can be directly observed from neutron crystal structures. For all the types of analysis performed, it is concluded that protection from exchange is only strongly correlated to secondary structure and the depth of the amide N atom.
Synopsis: Crystal structures of M. tuberculosis folylpolyglutamate synthetase complexed with two nucleotides have been determined at 2.0 and 2.3 Å resolution, revealing an active-site loop movement and associated changes that influence substrate binding.
Synopsis: Using idealized known RNA secondary-structural fragments, it is demonstrated that it is possible to solve novel complex RNA structures without resort to heavy-atom phasing methods.
Synopsis: Crystal structures of winged-bean basic agglutinin with disaccharides having glycosidic linkages that differ from those in the A and B blood-group substances reveal the structural basis for the higher specifity of the lectin for the blood-group antigens.
Synopsis: It is shown that the anisotropy of anomalous scattering (AAS) is a significant and ubiquitous effect in data sets collected at an absorption edge and that its exploitation can substantially enhance the phasing power of single- or multi-wavelength anomalous diffraction. The improvements in the phases are typically of the same order of magnitude as those obtained in a conventional approach by adding a second-wavelength data set to a SAD experiment.
Synopsis: Microporous molecular sieves were used as a hetero-epitaxic nucleant for protein crystallization.
Synopsis: The crystal structures of p38 MAP kinase complexed with two pyrrolotriazine-based inhibitors led to the elucidation of the high-affinity binding mode of these compounds.
Synopsis: The crystal structures of apo histidinol-phosphate aminotransferase from C. glutamicum, of the internal PLP aldimine adduct and of a pyridoxamine 5-phosphate-enzyme complex were determined at resolutions of 2.2, 2.1 and 1.8 Å, respectively. The residues lining the substrate-binding pocket were studied by site-directed mutagenesis.
Synopsis: Hybrid cluster proteins (HCP), whose function has yet to be determined, possess a similar fold to carbon monoxide dehydrogenases which also have a related metal-sulfur cluster at the equivalent hybrid cluster position. In HCP the precise nature of the hybrid cluster appears to be dependent on the absence or presence of oxygen during the purification and crystallization procedures.
Synopsis: An evaluation is made of the protonation states of surface Asp and Glu residues in the C1 domain of cMyBP-C at 1.3 Å resolution. Extrapolations are made of the X-ray diffraction resolution required and/or of the specimen volume required for neutron protein crystallography to determine such states precisely.
-enolase (hENO1), a multifunctional glycolytic enzymeSynopsis: The crystal structure of human -enolase (hENO1) has been determined for the first time and discloses distinct surface properties despite its high sequence similarities to other enolases. The surface properties provide an insight into its unique activities, including plasmin(ogen) and DNA binding, which are closely related to its roles in numerous diseases such as metastatic cancer, autoimmune disorders, ischaemia and bacterial infection.
Synopsis: The crystal structure of the enzymatically active domain of Ply500 has been solved at 1.8 Å resolution.
Synopsis: Human Fc fragments containing the L234F/L235E/P331S triple mutation exhibit a dramatic decrease in their binding to several effector molecules (CD64, CD32A, CD16 and C1q). The three-dimensional structure of such a mutated fragment reveals that these broad-ranging functional effects are not caused by major structural rearrangements in the Fc moiety.
Synopsis: The structure of the Fab fragment f3p4 selected from the HuCAL GOLD library is reported.
Synopsis: The crystal structure of M. tuberculosis phosphoribosyl-ATP pyrophosphohydrolase, the second enzyme in the histidine-biosynthetic pathway, is presented. The structural and inferred functional relationships between M. tuberculosis phosphoribosyl-ATP pyrophosphohydrolase and other members of the nucleoside-triphosphate pyrophosphatase-fold family are described.
Synopsis: The structure of mouse IP-10 shows a novel tetrameric association.
Synopsis: A method of automatically fitting nucleic acid double helices into electron density of high to medium resolution is presented and tested.
Synopsis: The crystal structure of an archaeal alanine:glyoxylate aminotransferase which has an amino-acid sequence that shows no similarity to any other known alanine:glyoxylate aminotransferases was determined.
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