1bj3

From Proteopedia

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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

Structural highlights

1bj3 is a 2 chain structure with sequence from Protobothrops flavoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SL9B_PROFL When linked to subunit A of IX/X-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factors IX (F9) and factor X (10) in the presence of calcium with a 1 to 1 stoichiometry. When linked to subunit A of IX-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (but not to factor X) in the presence of calcium with a 1 to 1 stoichiometry.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shikamoto Y, Morita T, Fujimoto Z, Mizuno H. Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein. J Biol Chem. 2003 Jun 27;278(26):24090-4. Epub 2003 Apr 14. PMID:12695512 doi:10.1074/jbc.M300650200
↑ Atoda H, Morita T. A novel blood coagulation factor IX/factor X-binding protein with anticoagulant activity from the venom of Trimeresurus flavoviridis (Habu snake): isolation and characterization. J Biochem. 1989 Nov;106(5):808-13. PMID:2613688
↑ Atoda H, Yoshida N, Ishikawa M, Morita T. Binding properties of the coagulation factor IX/factor X-binding protein isolated from the venom of Trimeresurus flavoviridis. Eur J Biochem. 1994 Sep 1;224(2):703-8. PMID:7925387
↑ Atoda H, Ishikawa M, Yoshihara E, Sekiya F, Morita T. Blood coagulation factor IX-binding protein from the venom of Trimeresurus flavoviridis: purification and characterization. J Biochem. 1995 Nov;118(5):965-73. PMID:8749314
↑ Mizuno H, Fujimoto Z, Koizumi M, Kano H, Atoda H, Morita T. 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. J Mol Biol. 1999 May 28;289(1):103-12. PMID:10339409 doi:http://dx.doi.org/10.1006/jmbi.1999.2756

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1bj3"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS==
-<StructureSection load='1bj3' size='340' side='right' caption='[[1bj3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='1bj3' size='340' side='right'caption='[[1bj3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trimeresurus_flavoviridis Trimeresurus 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BJ3 FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bj3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bj3 RCSB], [http://www.ebi.ac.uk/pdbsum/1bj3 PDBsum]</span></td></tr>
+<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>
+<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>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SL9B_PROFL SL9B_PROFL] When linked to subunit A of IX/X-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factors IX (F9) and factor X (10) in the presence of calcium with a 1 to 1 stoichiometry.  When linked to subunit A of IX-bp, anticoagulant protein which binds to the gamma-carboxyglutamic acid-domain regions of factor IX (but not to factor X) in the presence of calcium with a 1 to 1 stoichiometry.<ref>PMID:12695512</ref> <ref>PMID:2613688</ref> <ref>PMID:7925387</ref> <ref>PMID:8749314</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/1bj3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bj/1bj3_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1bj3" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Trimeresurus flavoviridis]]
+[[Category: Large Structures]]
-[[Category: Atoda, H]]
+[[Category: Protobothrops flavoviridis]]
-[[Category: Fujimoto, Z]]
+[[Category: Atoda H]]
-[[Category: Kano, H]]
+[[Category: Fujimoto Z]]
-[[Category: Koizumi, M]]
+[[Category: Kano H]]
-[[Category: Mizuno, H]]
+[[Category: Koizumi M]]
-[[Category: Morita, T]]
+[[Category: Mizuno H]]
-[[Category: C-type lectin superfamily]]
+[[Category: Morita T]]
-[[Category: Coagulation factor ix-binding]]
-[[Category: Collagen binding protein]]
-[[Category: Habu snake]]
-[[Category: Heterodimer]]
-[[Category: Venom]]

1bj3

From Proteopedia

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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