spacer
spacer

PDBsum entry 1oak
Go to PDB code: 
protein Protein-protein interface(s) links
Complex (willebrand/immunoglobulin) PDB id
1oak

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
212 a.a.
218 a.a. *
196 a.a. *
Waters ×366
* Residue conservation analysis
PDB id:
1oak
Name: Complex (willebrand/immunoglobulin)
Title: Crystal structure of the von willebrand factor (vwf) a1 domain in complex with the function blocking nmc-4 fab
Structure: Nmc-4 igg1. Chain: l. Fragment: fab fragment, an anti von willebrand factor (vwf) a1 domain. Engineered: yes. Other_details: the antibody heavy chain consists of two segments, h1 and h2, both labeled chain h in this entry. Nmc-4 igg1. Chain: h.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: hybridoma. Organ: blood. Expressed in: mus musculus. Expression_system_taxid: 10090. Expression_system_cell_line: mopc21. Homo sapiens.
Biol. unit: Trimer (from PQS)
Resolution:
2.20Å     R-factor:   0.201     R-free:   0.274
Authors: R.Celikel,K.I.Varughese
Key ref: R.Celikel et al. (1998). Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab. Nat Struct Biol, 5, 189-194. PubMed id: 9501911
Date:
18-Dec-97     Release date:   21-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 212 a.a.
Protein chain
Pfam   ArchSchema ?
P01868  (IGHG1_MOUSE) -  Ig gamma-1 chain C region secreted form from Mus musculus
Seq:
Struc: 		324 a.a.
218 a.a.*
Protein chain
Pfam   ArchSchema ?
P04275  (VWF_HUMAN) -  von Willebrand factor from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2813 a.a.
196 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
Nat Struct Biol 5:189-194 (1998)
PubMed id: 9501911  
 
 
Crystal structure of the von Willebrand factor A1 domain in complex with the function blocking NMC-4 Fab.
R.Celikel, K.I.Varughese, Madhusudan, A.Yoshioka, J.Ware, Z.M.Ruggeri.
 
  ABSTRACT  
 
The presence of one or more copies of von Willebrand factor type A domains identifies a superfamily of proteins usually involved in biological processes controlled by specific molecular interactions, often adhesive in nature. We have solved the crystal structure of the prototypic von Willebrand factor A1 domain, essential for the antihemorrhagic activity of platelets, in complex with the function blocking antibody, NMC-4, at 2.2 A resolution. This has led to the recognition of a putative binding groove for the platelet receptor, glycoprotein Ib alpha, formed by two adjacent alpha-helices and a beta-strand. The structure also shows a contact interface between A1 domain pairs, suggesting a hypothetical mechanism for the regulation of protein assembly and heterologous ligand binding mediated by homophilic interactions of type A domains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19619477 M.Auton, E.Sedlák, J.Marek, T.Wu, C.Zhu, and M.A.Cruz (2009).
Changes in thermodynamic stability of von Willebrand factor differentially affect the force-dependent binding to platelet GPIbalpha.
  Biophys J, 97, 618-627.  
19913482 R.H.Huang, D.H.Fremont, J.L.Diener, R.G.Schaub, and J.E.Sadler (2009).
A structural explanation for the antithrombotic activity of ARC1172, a DNA aptamer that binds von Willebrand factor domain A1.
  Structure, 17, 1476-1484.
PDB codes: 3hxo 3hxq
18369690 T.Nakayama, T.Matsushita, K.Yamamoto, N.Mutsuga, T.Kojima, A.Katsumi, N.Nakao, J.E.Sadler, T.Naoe, and H.Saito (2008).
Identification of amino acid residues responsible for von Willebrand factor binding to sulfatide by charged-to-alanine-scanning mutagenesis.
  Int J Hematol, 87, 363-370.  
18622395 Y.Miyamoto, D.Shi, M.Nakajima, K.Ozaki, A.Sudo, A.Kotani, A.Uchida, T.Tanaka, N.Fukui, T.Tsunoda, A.Takahashi, Y.Nakamura, Q.Jiang, and S.Ikegawa (2008).
Common variants in DVWA on chromosome 3p24.3 are associated with susceptibility to knee osteoarthritis.
  Nat Genet, 40, 994-998.  
16449527 A.J.Reininger, H.F.Heijnen, H.Schumann, H.M.Specht, W.Schramm, and Z.M.Ruggeri (2006).
Mechanism of platelet adhesion to von Willebrand factor and microparticle formation under high shear stress.
  Blood, 107, 3537-3545.  
16892470 Y.Singh, G.T.Dolphin, J.Razkin, and P.Dumy (2006).
Synthetic Peptide templates for molecular recognition: recent advances and applications.
  Chembiochem, 7, 1298-1314.  
16772609 Z.M.Ruggeri, J.N.Orje, R.Habermann, A.B.Federici, and A.J.Reininger (2006).
Activation-independent platelet adhesion and aggregation under elevated shear stress.
  Blood, 108, 1903-1910.  
15174170 J.Hauert, J.Fernandez-Carneado, O.Michielin, S.Mathieu, D.Grell, M.Schapira, O.Spertini, M.Mutter, G.Tuchscherer, and T.Kovacsovics (2004).
A template-assembled synthetic protein surface mimetic of the von Willebrand factor A1 domain inhibits botrocetin-induced platelet aggregation.
  Chembiochem, 5, 856-864.  
15030285 A.Bonnefoy, J.Vermylen, and M.F.Hoylaerts (2003).
Inhibition of von Willebrand factor-GPIb/IX/V interactions as a strategy to prevent arterial thrombosis.
  Expert Rev Cardiovasc Ther, 1, 257-269.  
12871332 G.Borthakur, M.A.Cruz, J.F.Dong, L.McIntire, F.Li, J.A.López, and P.Thiagarajan (2003).
Sulfatides inhibit platelet adhesion to von Willebrand factor in flowing blood.
  J Thromb Haemost, 1, 1288-1295.  
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.  
11756664 B.Savage, J.J.Sixma, and Z.M.Ruggeri (2002).
Functional self-association of von Willebrand factor during platelet adhesion under flow.
  Proc Natl Acad Sci U S A, 99, 425-430.  
12220170 D.W.Chung, and K.Fujikawa (2002).
Processing of von Willebrand factor by ADAMTS-13.
  Biochemistry, 41, 11065-11070.  
12183630 E.G.Huizinga, S.Tsuji, R.A.Romijn, M.E.Schiphorst, P.G.de Groot, J.J.Sixma, and P.Gros (2002).
Structures of glycoprotein Ibalpha and its complex with von Willebrand factor A1 domain.
  Science, 297, 1176-1179.
PDB codes: 1m0z 1m10
12022870 G.Rastegar-Lari, B.O.Villoutreix, A.S.Ribba, P.Legendre, D.Meyer, and D.Baruch (2002).
Two clusters of charged residues located in the electropositive face of the von Willebrand factor A1 domain are essential for heparin binding.
  Biochemistry, 41, 6668-6678.  
  12102729 J.E.Garbarino, and I.R.Gibbons (2002).
Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein.
  BMC Genomics, 3, 18.  
12121649 K.Fukuda, T.A.Doggett, L.A.Bankston, M.A.Cruz, T.G.Diacovo, and R.C.Liddington (2002).
Structural basis of von Willebrand factor activation by the snake toxin botrocetin.
  Structure, 10, 943-950.
PDB codes: 1ijb 1ijk
11843285 M.Sugimoto, and S.Miyata (2002).
Functional property of von Willebrand factor under flowing blood.
  Int J Hematol, 75, 19-24.  
11943773 T.Nakayama, T.Matsushita, Z.Dong, J.E.Sadler, S.Jorieux, C.Mazurier, D.Meyer, T.Kojima, and H.Saito (2002).
Identification of the regulatory elements of the human von Willebrand factor for binding to platelet GPIb. Importance of structural integrity of the regions flanked by the CYS1272-CYS1458 disulfide bond.
  J Biol Chem, 277, 22063-22072.  
10706763 D.A.Facey, E.J.Favaloro, E.Maxwell, R.Baker, and M.S.Hertzberg (2000).
Type 2B von Willebrand's disease in thirteen individuals from five unrelated Australian families: phenotype and genotype correlations.
  Am J Hematol, 63, 197-199.  
11304672 J.Fernandez-Carneado, D.Grell, P.Durieux, J.Hauert, T.Kovacsovics, and G.Tuchscherer (2000).
Surface grafting onto template-assembled synthetic protein scaffolds in molecular recognition.
  Biopolymers, 55, 451-458.  
11193052 P.B.Furtado, R.Furmonaviciene, J.McElveen, H.F.Sewell, and F.Shakib (2000).
Prediction of the interacting surfaces in a trimolecular complex formed between the major dust mite allergen Der p 1, a mouse monoclonal anti-Der p 1 antibody, and its anti-idiotype.
  Mol Pathol, 53, 324-332.  
10777573 S.Vasudevan, J.R.Roberts, R.A.McClintock, J.A.Dent, R.Celikel, J.Ware, K.I.Varughese, and Z.M.Ruggeri (2000).
Modeling and functional analysis of the interaction between von Willebrand factor A1 domain and glycoprotein Ibalpha.
  J Biol Chem, 275, 12763-12768.  
10753907 T.Matsushita, D.Meyer, and J.E.Sadler (2000).
Localization of von willebrand factor-binding sites for platelet glycoprotein Ib and botrocetin by charged-to-alanine scanning mutagenesis.
  J Biol Chem, 275, 11044-11049.  
10233434 D.A.Facey, E.J.Favaloro, J.Koutts, M.C.Berndt, and M.S.Hertzberg (1999).
Identification and characterization of a novel mutation in von Willebrand factor causing type 2B von Willebrand's disease.
  Br J Haematol, 105, 538-541.  
10224097 D.Piecha, S.Muratoglu, M.Mörgelin, N.Hauser, D.Studer, I.Kiss, M.Paulsson, and F.Deák (1999).
Matrilin-2, a large, oligomeric matrix protein, is expressed by a great variety of cells and forms fibrillar networks.
  J Biol Chem, 274, 13353-13361.  
9915842 M.Mazzucato, P.Spessotto, A.Masotti, L.De Appollonia, M.R.Cozzi, A.Yoshioka, R.Perris, A.Colombatti, and L.De Marco (1999).
Identification of domains responsible for von Willebrand factor type VI collagen interaction mediating platelet adhesion under high flow.
  J Biol Chem, 274, 3033-3041.  
10037753 S.Miyata, and Z.M.Ruggeri (1999).
Distinct structural attributes regulating von Willebrand factor A1 domain interaction with platelet glycoprotein Ibalpha under flow.
  J Biol Chem, 274, 6586-6593.  
10542245 T.Kamata, R.C.Liddington, and Y.Takada (1999).
Interaction between collagen and the alpha(2) I-domain of integrin alpha(2)beta(1). Critical role of conserved residues in the metal ion-dependent adhesion site (MIDAS) region.
  J Biol Chem, 274, 32108-32111.  
9741630 B.Savage, F.Almus-Jacobs, and Z.M.Ruggeri (1998).
Specific synergy of multiple substrate-receptor interactions in platelet thrombus formation under flow.
  Cell, 94, 657-666.  
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.

 

spacer
spacer