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1bj3

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(New page: 200px<br /><applet load="1bj3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bj3, resolution 2.6&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
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[[Image:1bj3.gif|left|200px]]<br /><applet load="1bj3" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bj3, resolution 2.6&Aring;" />
 
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'''CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS==
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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.
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<StructureSection load='1bj3' size='340' side='right'caption='[[1bj3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1bj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Protobothrops_flavoviridis Protobothrops flavoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BJ3 FirstGlance]. <br>
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1BJ3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus flavoviridis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BJ3 OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bj3 OCA], [https://pdbe.org/1bj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bj3 RCSB], [https://www.ebi.ac.uk/pdbsum/1bj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bj3 ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10339409 10339409]
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</table>
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[[Category: Protein complex]]
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== Function ==
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[[Category: Trimeresurus flavoviridis]]
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[https://www.uniprot.org/uniprot/SLA_PROFL SLA_PROFL] Anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (F9) (but not factor X) in the presence of calcium with a 1 to 1 stoichiometry.<ref>PMID:12695512</ref> <ref>PMID:8749314</ref>
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[[Category: Atoda, H.]]
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== Evolutionary Conservation ==
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[[Category: Fujimoto, Z.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Kano, H.]]
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Check<jmol>
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[[Category: Koizumi, M.]]
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<jmolCheckbox>
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[[Category: Mizuno, H.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/1bj3_consurf.spt"</scriptWhenChecked>
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[[Category: Morita, T.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: CA]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: c-type lectin superfamily]]
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</jmolCheckbox>
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[[Category: coagulation factor ix-binding]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bj3 ConSurf].
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[[Category: habu snake]]
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<div style="clear:both"></div>
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[[Category: heterodimer]]
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== References ==
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[[Category: venom]]
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<references/>
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__TOC__
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:41:23 2007''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Protobothrops flavoviridis]]
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[[Category: Atoda H]]
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[[Category: Fujimoto Z]]
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[[Category: Kano H]]
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[[Category: Koizumi M]]
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[[Category: Mizuno H]]
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[[Category: Morita T]]

Current revision

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

PDB ID 1bj3

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