1bj3

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spinqualitylabelsall models 1bj3, resolution 2.6Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS

Overview

Coagulation factor IX-binding protein (IX-bp) isolated from the venom of, the habu snake (Trimeresurus flavoviridis) is a disulfide-linked, heterodimer consisting of homologous subunits A and B. The structure of, IX-bp has been solved by X-ray crystallography at 2.6 A resolution to a, crystallographic R -value of 0.181. The main-chain fold of each subunit is, homologous to the carbohydrate-recognition domain of C-type lectins, (C-type CRDs) except for the extended central loop. The structure is, almost identical with that of factors IX and X-binding protein (IX/X-bp), as expected from the high level of amino acid sequence homology. The, functional difference in ligand recognition from IX/X-bp must reside in, the amino acid differences. A continuity of different amino acid residues, located from the C-terminal of the second alpha-helix to the following, loop forms the local conformational difference in this region between the, two proteins. This loop participates in the formation of the concave, surface between the two subunits, the putative binding site for the, Gla-domain (gamma-carboxyglutamic acid-containing domain) of the, coagulation factors. Another difference between the two proteins is in the, relative disposition of subunits A and B. When the B subunits are, superimposed, about a 6 degrees rotation is required for the superposition, of the A subunits. A calcium ion links the second alpha-helix region to, the C-terminal tail in each subunit and helps to stabilize the structure, for Gla-domain binding. The interface created by the central loop swapping, in the dimer IX-bp is almost identical with that seen within the monomeric, C-type CRDs. This dimer forms as the result of the amino acid deletion in, the linker region of the central loop of the original C-type lectins. Such, a dimerization disrupts the lectin active site and creates a Gla-domain, binding site, imparting functional diversity.

About this Structure

1BJ3 is a Protein complex structure of sequences from Trimeresurus flavoviridis with CA as ligand. Full crystallographic information is available from OCA.

Reference

Crystal structure of coagulation factor IX-binding protein from habu snake venom at 2.6 A: implication of central loop swapping based on deletion in the linker region., Mizuno H, Fujimoto Z, Koizumi M, Kano H, Atoda H, Morita T, J Mol Biol. 1999 May 28;289(1):103-12. PMID:10339409

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