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Immune system PDB id
1fe8
Jmol
Contents
Protein chains
190 a.a. *
210 a.a. *
211 a.a. *
Ligands
NAG-FUC ×3
NAG ×2
CAC
Waters ×878
* Residue conservation analysis
PDB id:
1fe8
Name: Immune system
Title: Crystal structure of the von willebrand factor a3 domain in with a fab fragment of igg ru5 that inhibits collagen bindi
Structure: Von willebrand factor. Chain: a, b, c. Fragment: collagen binding domain a3. Engineered: yes. Immunoglobulin igg ru5. Chain: h, i, j. Fragment: fab fragment heavy chain. Immunoglobulin igg ru5. Chain: l, m, n.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Hexamer (from PQS)
Resolution:
2.03Å     R-factor:   0.227     R-free:   0.264
Authors: B.Bouma,E.G.Huizinga,M.E.Schiphorst,J.J.Sixma,J.Kroon,P.Gros
Key ref:
R.A.Romijn et al. (2001). Identification of the collagen-binding site of the von Willebrand factor A3-domain. J Biol Chem, 276, 9985-9991. PubMed id: 11098050 DOI: 10.1074/jbc.M006548200
Date:
21-Jul-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04275  (VWF_HUMAN) -  von Willebrand factor
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2813 a.a.
190 a.a.
Protein chain
No UniProt id for this chain
Protein chain
No UniProt id for this chain
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein binding     1 term  

 

 
DOI no: 10.1074/jbc.M006548200 J Biol Chem 276:9985-9991 (2001)
PubMed id: 11098050  
 
 
Identification of the collagen-binding site of the von Willebrand factor A3-domain.
R.A.Romijn, B.Bouma, W.Wuyster, P.Gros, J.Kroon, J.J.Sixma, E.G.Huizinga.
 
  ABSTRACT  
 
Von Willebrand factor (vWF) is a multimeric glycoprotein that mediates platelet adhesion and thrombus formation at sites of vascular injury. vWF functions as a molecular bridge between collagen and platelet receptor glycoprotein Ib. The major collagen-binding site of vWF is contained within the A3 domain, but its precise location is unknown. To localize the collagen-binding site, we determined the crystal structure of A3 in complex with an Fab fragment of antibody RU5 that inhibits collagen binding. The structure shows that RU5 recognizes a nonlinear epitope consisting of residues 962-966, 981-997, and 1022-1026. Alanine mutants were constructed of residues Arg(963), Glu(987), His(990), Arg(1016), and His(1023), located in or close to the epitope. Mutants were expressed as fully processed multimeric vWF. Mutation of His(1023) abolished collagen binding, whereas mutation of Arg(963) and Arg(1016) reduced collagen binding by 25-35%. These residues are part of loops alpha3beta4 and alpha1beta2 and alpha-helix 3, respectively, and lie near the bottom face of the domain. His(1023) and flanking residues display multiple conformations in available A3-crystal structures, suggesting that binding of A3 to collagen involves an induced-fit mechanism. The collagen-binding site of A3 is located distant from the top face of the domain where collagen-binding sites are found in homologous integrin I domains.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Structural overlay of C[ ]traces of the three A3·RU5 Fab complexes in the asymmetric unit. For calculation of the best superposition, C[ ]atoms of A3 and variable domains of RU5-Fab were used. The A3·RU5 interaction region is well conserved among the three complexes, but relatively large differences are shown in orientations of the RU5 constant domains with respect to its variable domains and A3. The diagram was generated with MOLSCRIPT (43). 		Figure 3.
Fig. 3. Ribbon diagram of A3 and RU5 variable domains. Residues of A3 that are part of the epitope of RU5 are indicated by yellow spheres. Regions of RU5 CDRs that interact with A3 are color-coded in light blue. Regions of A3 that show different conformations among four crystal structures are shown in purple trace. Disulfide bond Cys923-Cys1109 is shown in green ball-and-stick. The -helices and -strands of A3 are depicted in blue and red, respectively. For clarity, -helix 2 is not shown by a ribbon but in "coil" representation. The V[H] domain of RU5 is in brown; the V[L] domain is in green. The diagram was generated with MOLSCRIPT (43) and RASTER3D (44).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 9985-9991) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20351310 N.Pugh, A.M.Simpson, P.A.Smethurst, P.G.de Groot, N.Raynal, and R.W.Farndale (2010).
Synergism between platelet collagen receptors defined using receptor-specific collagen-mimetic peptide substrata in flowing blood.
  Blood, 115, 5069-5079.  
19687512 A.F.Riddell, K.Gomez, C.M.Millar, G.Mellars, S.Gill, S.A.Brown, M.Sutherland, M.A.Laffan, and T.A.McKinnon (2009).
Characterization of W1745C and S1783A: 2 novel mutations causing defective collagen binding in the A3 domain of von Willebrand factor.
  Blood, 114, 3489-3496.  
19175495 S.Tasneem, F.Adam, I.Minullina, M.Pawlikowska, S.K.Hui, S.Zheng, J.L.Miller, and C.P.Hayward (2009).
Platelet adhesion to multimerin 1 in vitro: influences of platelet membrane receptors, von Willebrand factor and shear.
  J Thromb Haemost, 7, 685-692.  
  18512339 V.B.Carruthers, and F.M.Tomley (2008).
Microneme proteins in apicomplexans.
  Subcell Biochem, 47, 33-45.  
17635730 R.W.Farndale, D.A.Slatter, P.R.Siljander, and G.E.Jarvis (2007).
Platelet receptor recognition and cross-talk in collagen-induced activation of platelets.
  J Thromb Haemost, 5, 220-229.  
16805860 A.Bonnefoy, R.A.Romijn, P.A.Vandervoort, I.VAN Rompaey, J.Vermylen, and M.F.Hoylaerts (2006).
von Willebrand factor A1 domain can adequately substitute for A3 domain in recruitment of flowing platelets to collagen.
  J Thromb Haemost, 4, 2151-2161.  
16839359 B.Obert, R.A.Romijn, A.Houllier, E.G.Huizinga, and J.P.Girma (2006).
Characterization of bitiscetin-2, a second form of bitiscetin from the venom of Bitis arietans : comparison of its binding site with the collagen-binding site on the von Willebrand factor A3-domain.
  J Thromb Haemost, 4, 1596-1601.  
16454628 E.P.Sabino, H.N.Erb, and J.L.Catalfamo (2006).
Development of a collagen-binding activity assay as a screening test for type II von Willebrand disease in dogs.
  Am J Vet Res, 67, 242-249.  
16999849 J.Chen, and J.A.López (2006).
New light on an old story: von Willebrand factor binding to collagen.
  J Thromb Haemost, 4, 2148-2150.  
17098186 T.A.Springer (2006).
Complement and the multifaceted functions of VWA and integrin I domains.
  Structure, 14, 1611-1616.  
15946218 P.E.Litjens, G.Van Willigen, C.Weeterings, M.J.Ijsseldijk, M.Van Lier, E.Koivunen, C.G.Gahmberg, and J.W.Akkerman (2005).
A tripeptide mimetic of von Willebrand factor residues 981-983 enhances platelet adhesion to fibrinogen by signaling through integrin alpha(IIb)beta3.
  J Thromb Haemost, 3, 1274-1283.  
15016353 A.A.Bhattacharya, M.L.Lupher, D.E.Staunton, and R.C.Liddington (2004).
Crystal structure of the A domain from complement factor B reveals an integrin-like open conformation.
  Structure, 12, 371-378.
PDB code: 1q0p
15146485 M.Geva, M.Eisenstein, and L.Addadi (2004).
Antibody recognition of chiral surfaces. Structural models of antibody complexes with leucine-leucine-tyrosine crystal surfaces.
  Proteins, 55, 862-873.  
15102010 R.W.Farndale, J.J.Sixma, M.J.Barnes, and P.G.de Groot (2004).
The role of collagen in thrombosis and hemostasis.
  J Thromb Haemost, 2, 561-573.  
12447349 N.Nishida, H.Sumikawa, M.Sakakura, N.Shimba, H.Takahashi, H.Terasawa, E.Suzuki, and I.Shimada (2003).
Collagen-binding mode of vWF-A3 domain determined by a transferred cross-saturation experiment.
  Nat Struct Biol, 10, 53-58.  
12871266 Z.M.Ruggeri (2003).
Von Willebrand factor, platelets and endothelial cell interactions.
  J Thromb Haemost, 1, 1335-1342.  
12579041 Z.M.Ruggeri (2003).
Von Willebrand factor.
  Curr Opin Hematol, 10, 142-149.  
12388743 C.A.Whittaker, and R.O.Hynes (2002).
Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere.
  Mol Biol Cell, 13, 3369-3387.  
11843287 C.V.Denis (2002).
Molecular and cellular biology of von Willebrand factor.
  Int J Hematol, 75, 3-8.  
11468390 E.G.Huizinga, A.Schouten, T.M.Connolly, J.Kroon, J.J.Sixma, and P.Gros (2001).
The structure of leech anti-platelet protein, an inhibitor of haemostasis.
  Acta Crystallogr D Biol Crystallogr, 57, 1071-1078.
PDB code: 1i8n
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 code is shown on the right.