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PDBsum entry 1bj3
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protein metals Protein-protein interface(s) links
Collagen binding protein PDB id
1bj3

 

 

 

 

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Contents
Protein chains
129 a.a. *
123 a.a. *
Metals
_CA ×2
Waters ×83
* Residue conservation analysis
PDB id:
1bj3
Name: Collagen binding protein
Title: Crystal structure of coagulation factor ix-binding protein (ix-bp) from venom of habu snake with a heterodimer of c-type lectin domains
Structure: Protein (coagulation factor ix-binding protein a). Chain: a. Fragment: c-type lectin crd domain. Synonym: ix-bp. Other_details: disulphide dimer between a cys79 and b cys75, protein composed of homologous subunits to the carbohydrate recognition domain of c-type lectin. Protein (coagulation factor ix-binding protein b). Chain: b.
Source: Trimeresurus flavoviridis. Organism_taxid: 88087. Secretion: venom. Secretion: venom
Biol. unit: Hetero-Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.182     R-free:   0.271
Authors: H.Mizuno,Z.Fujimoto,M.Koizumi,H.Kano,H.Atoda,T.Morita
Key ref:
H.Mizuno et al. (1999). 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, 289, 103-112. PubMed id: 10339409 DOI: 10.1006/jmbi.1999.2756
Date:
02-Jul-98     Release date:   16-Aug-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7LZ71  (SLA_PROFL) -  Snaclec coagulation factor IX-binding protein subunit A from Protobothrops flavoviridis
Seq:
Struc: 		129 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P23807  (SL9B_PROFL) -  Snaclec coagulation factor IX/factor X-binding protein subunit B from Protobothrops flavoviridis
Seq:
Struc: 		146 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1006/jmbi.1999.2756 J Mol Biol 289:103-112 (1999)
PubMed id: 10339409  
 
 
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.
H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, H.Atoda, T.Morita.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Geometry around the Ca 2+ -binding sites: (a) subunit A; (b) subunit B. White, blue and red lines show car- bon, nitrogen and oxygen atoms, respectively. 		Figure 6.
Figure 6. Comparison of hydrophobic interactions in the C-interfaces between IX-bp (top) and MBP (bottom). Asn76 to Ala91 in the CLR of subunit B interacts with amino acid residues in the body of subunit A (pink) in IX-bp. In MBP, Gln167 to Lys182 in the CLR interacts with amino acid residues in the body (pink). Amino acid residues par- ticipating in the hydrophobic interactions are labeled.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 289, 103-112) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21197556 D.Shen, X.Xu, H.Wu, L.Peng, Y.Zhang, J.Song, and Q.Su (2011).
Metal ion binding to anticoagulation factor II from the venom of Agkistrodon acutus: stabilization of the structure and regulation of the binding affinity to activated coagulation factor X.
  J Biol Inorg Chem, 16, 523-537.  
  20180816 Y.Z.Ohkubo, J.H.Morrissey, and E.Tajkhorshid (2010).
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor.
  J Thromb Haemost, 8, 1044-1053.  
19184130 X.Xu, L.Zhang, D.Shen, H.Wu, L.Peng, and J.Li (2009).
Effect of metal ion substitutions in anticoagulation factor I from the venom of Agkistrodon acutus on the binding of activated coagulation factor X and on structural stability.
  J Biol Inorg Chem, 14, 559-571.  
17473009 J.Brown, C.A.O'Callaghan, A.S.Marshall, R.J.Gilbert, C.Siebold, S.Gordon, G.D.Brown, and E.Y.Jones (2007).
Structure of the fungal beta-glucan-binding immune receptor dectin-1: implications for function.
  Protein Sci, 16, 1042-1052.
PDB codes: 2bpd 2bpe 2bph 2cl8
17279335 X.Xu, J.Chen, L.Zhang, S.Wang, D.Shen, and Q.Liu (2007).
Calcium ion-induced stabilization and refolding of agkisacutacin from Agkistrodon acutus venom studied by fluorescent spectroscopy.
  J Fluoresc, 17, 215-221.  
16475157 X.L.Xu, J.X.Chen, L.Y.Zhang, X.H.Liu, W.Q.Liu, and Q.L.Liu (2006).
Effects of rare earth ions on the conformational stability of anticoagulation factor II from Agkistrodon acutus venom probed by fluorescent spectroscopy.
  Biopolymers, 82, 167-175.  
16206329 A.Bazaa, N.Marrakchi, M.El Ayeb, L.Sanz, and J.J.Calvete (2005).
Snake venomics: comparative analysis of the venom proteomes of the Tunisian snakes Cerastes cerastes, Cerastes vipera and Macrovipera lebetina.
  Proteomics, 5, 4223-4235.  
  16508118 N.Suzuki, Y.Shikamoto, Z.Fujimoto, T.Morita, and H.Mizuno (2005).
Crystallization and preliminary X-ray analysis of coagulation factor IX-binding protein from habu snake venom at pH 6.5 and 4.6.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 147-149.  
15576563 P.Paaventhan, C.Kong, J.S.Joseph, M.C.Chung, and P.R.Kolatkar (2005).
Structure of rhodocetin reveals noncovalently bound heterodimer interface.
  Protein Sci, 14, 169-175.
PDB code: 1sb2
16102046 Q.Lu, J.M.Clemetson, and K.J.Clemetson (2005).
Snake venoms and hemostasis.
  J Thromb Haemost, 3, 1791-1799.  
15502319 G.Xu, M.Teng, L.Niu, P.Liu, Y.Dong, Q.Liu, Q.Huang, and Q.Hao (2004).
Purification, characterization, crystallization and preliminary X-ray crystallographic analysis of two novel C-type lectin-like proteins: Aall-A and Aall-B from Deinagkistrodon acutus venom.
  Acta Crystallogr D Biol Crystallogr, 60, 2035-2037.  
15319425 H.Sugawara, M.Kusunoki, G.Kurisu, T.Fujimoto, H.Aoyagi, and T.Hatakeyama (2004).
Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis.
  J Biol Chem, 279, 45219-45225.
PDB codes: 1wmy 1wmz
14684891 T.Batuwangala, M.Leduc, J.M.Gibbins, C.Bon, and E.Y.Jones (2004).
Structure of the snake-venom toxin convulxin.
  Acta Crystallogr D Biol Crystallogr, 60, 46-53.
PDB code: 1uos
15005338 T.Morita (2004).
Use of snake venom inhibitors in studies of the function and tertiary structure of coagulation factors.
  Int J Hematol, 79, 123-129.  
12657795 J.Zang, M.Teng, and L.Niu (2003).
Purification, crystallization and preliminary crystallographic analysis of AHP IX-bp, a zinc ion and pH-dependent coagulation factor IX binding protein from Agkistrodon halys Pallas venom.
  Acta Crystallogr D Biol Crystallogr, 59, 730-733.  
14580195 K.Horii, D.Okuda, T.Morita, and H.Mizuno (2003).
Structural characterization of EMS16, an antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus.
  Biochemistry, 42, 12497-12502.
PDB code: 1ukm
12851390 N.Maita, K.Nishio, E.Nishimoto, T.Matsui, Y.Shikamoto, T.Morita, J.E.Sadler, and H.Mizuno (2003).
Crystal structure of von Willebrand factor A1 domain complexed with snake venom, bitiscetin: insight into glycoprotein Ibalpha binding mechanism induced by snake venom proteins.
  J Biol Chem, 278, 37777-37781.
PDB code: 1uex
12695512 Y.Shikamoto, T.Morita, Z.Fujimoto, and H.Mizuno (2003).
Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein.
  J Biol Chem, 278, 24090-24094.
PDB codes: 1j34 1j35
11861620 K.Natarajan, N.Dimasi, J.Wang, R.A.Mariuzza, and D.H.Margulies (2002).
Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
  Annu Rev Immunol, 20, 853-885.  
11914494 S.Liu, Z.Zhu, J.Sun, Z.Zhu, Q.Huang, M.Teng, and L.Niu (2002).
Purification, crystallization and preliminary X-ray crystallographic analysis of agkaggregin, a C-type lectin-like protein from Agkistrodon acutus venom.
  Acta Crystallogr D Biol Crystallogr, 58, 675-678.  
11910037 X.Xu, Q.Liu, H.Yu, and Y.Xie (2002).
Ca(II)- and Tb(III)-induced stabilization and refolding of anticoagulation factor I from the venom of Agkistrodon acutus.
  Protein Sci, 11, 944-956.  
11404471 H.Mizuno, Z.Fujimoto, H.Atoda, and T.Morita (2001).
Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.
  Proc Natl Acad Sci U S A, 98, 7230-7234.
PDB code: 1iod
10933804 C.Marcinkiewicz, R.R.Lobb, M.M.Marcinkiewicz, J.L.Daniel, J.B.Smith, C.Dangelmaier, P.H.Weinreb, D.A.Beacham, and S.Niewiarowski (2000).
Isolation and characterization of EMS16, a C-lectin type protein from Echis multisquamatus venom, a potent and selective inhibitor of the alpha2beta1 integrin.
  Biochemistry, 39, 9859-9867.  
10531492 K.Fukuda, H.Mizuno, H.Atoda, and T.Morita (1999).
Crystallization and preliminary x-ray studies of flavocetin-A, a platelet glycoprotein Ib-binding protein from the habu snake venom.
  Acta Crystallogr D Biol Crystallogr, 55, 1911-1913.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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