PDBsum entry 1n8e

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protein links
Blood clotting PDB id
Protein chains
74 a.a.* *
307 a.a.* *
295 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
Name: Blood clotting
Title: Fragment double-d from human fibrin
Structure: Fibrin alpha/alpha-e chain. Chain: a, d. Fragment: double-d alpha chain. Fibrin beta chain. Chain: b, e. Fragment: double-d beta chain. Fibrin gamma chain. Chain: c, f. Fragment: double-d gamma chain.
Source: Homo sapiens. Human. Organism_taxid: 9606. Other_details: fibrinogen prepared from blood bank plasma. Other_details: fibrinogen prepared from blood bank plasma
4.50Å     R-factor:   0.415     R-free:   0.416
Authors: Z.Yang,L.Pandi,R.F.Doolittle
Key ref:
Z.Yang et al. (2002). The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface. Biochemistry, 41, 15610-15617. PubMed id: 12501189 DOI: 10.1021/bi026666i
20-Nov-02     Release date:   07-Jan-03    

Protein chains
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
866 a.a.
74 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
491 a.a.
307 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
453 a.a.
295 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     fibrinogen complex   1 term 
  Biological process     signal transduction   3 terms 
  Biochemical function     receptor binding     2 terms  


DOI no: 10.1021/bi026666i Biochemistry 41:15610-15617 (2002)
PubMed id: 12501189  
The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.
Z.Yang, L.Pandi, R.F.Doolittle.
The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17090548 A.A.Amelot, M.Tagzirt, G.Ducouret, R.L.Kuen, and B.F.Le Bonniec (2007).
Platelet factor 4 (CXCL4) seals blood clots by altering the structure of fibrin.
  J Biol Chem, 282, 710-720.  
16373473 J.H.Brown (2006).
Breaking symmetry in protein dimers: designs and functions.
  Protein Sci, 15, 1.  
16051597 J.Cho, J.L.Degen, B.S.Coller, and D.F.Mosher (2005).
Fibrin but not adsorbed fibrinogen supports fibronectin assembly by spread platelets. Effects of the interaction of alphaIIb beta3 with the C terminus of the fibrinogen gamma-chain.
  J Biol Chem, 280, 35490-35498.  
15009453 J.W.Weisel (2004).
Cross-linked gamma-chains in fibrin fibrils bridge transversely between strands: no.
  J Thromb Haemost, 2, 394-399.  
15009452 M.W.Mosesson (2004).
Cross-linked gamma-chains in fibrin fibrils bridge 'transversely' between strands: yes.
  J Thromb Haemost, 2, 388-393.  
15099268 R.F.Doolittle (2004).
Determining the crystal structure of fibrinogen.
  J Thromb Haemost, 2, 683-689.  
12871291 R.F.Doolittle (2003).
X-ray crystallographic studies on fibrinogen and fibrin.
  J Thromb Haemost, 1, 1559-1565.  
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