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PDBsum entry 3ghg

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protein ligands metals Protein-protein interface(s) links
Blood clotting PDB id
3ghg
Jmol
Contents
Protein chains
174 a.a. *
401 a.a. *
381 a.a. *
186 a.a. *
Ligands
GLY-PRO-ARG-PRO ×4
GLY-HIS-ARG-PRO ×4
NAG-NDG-BMA-MAN-
NDG-MAN-NDG-GAL-
SIA-GAL-SIA
×3
NAG-NDG-BMA-MAN-
MAN
NAG-NAG
Metals
_CA ×8
* Residue conservation analysis
PDB id:
3ghg
Name: Blood clotting
Title: Crystal structure of human fibrinogen
Structure: Fibrinogen alpha chain. Chain: a, d, g, j. Fragment: mature chain. Synonym: fibrinopeptide a. Fibrinogen beta chain. Chain: b, e, h, k. Fragment: mature chain. Synonym: fibrinopeptide b. Fibrinogen gamma chain.
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood plasma. Synthetic: yes. Synthetic: yes
Resolution:
2.90Å     R-factor:   0.255     R-free:   0.309
Authors: R.F.Doolittle,J.M.Kollman,M.R.Sawaya,L.Pandi,M.Riley
Key ref: J.M.Kollman et al. (2009). Crystal structure of human fibrinogen. Biochemistry, 48, 3877-3886. PubMed id: 19296670
Date:
03-Mar-09     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
174 a.a.
Protein chains
Pfam   ArchSchema ?
P02675  (FIBB_HUMAN) -  Fibrinogen beta chain
Seq:
Struc:
491 a.a.
401 a.a.
Protein chains
Pfam   ArchSchema ?
P02679  (FIBG_HUMAN) -  Fibrinogen gamma chain
Seq:
Struc:
453 a.a.
381 a.a.
Protein chain
Pfam   ArchSchema ?
P02671  (FIBA_HUMAN) -  Fibrinogen alpha chain
Seq:
Struc:
 
Seq:
Struc:
866 a.a.
186 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   12 terms 
  Biological process     cellular response to leptin stimulus   22 terms 
  Biochemical function     structural molecule activity     7 terms  

 

 
Biochemistry 48:3877-3886 (2009)
PubMed id: 19296670  
 
 
Crystal structure of human fibrinogen.
J.M.Kollman, L.Pandi, M.R.Sawaya, M.Riley, R.F.Doolittle.
 
  ABSTRACT  
 
A crystal structure of human fibrinogen has been determined at approximately 3.3 A resolution. The protein was purified from human blood plasma, first by a cold ethanol precipitation procedure and then by stepwise chromatography on DEAE-cellulose. A product was obtained that was homogeneous on SDS-polyacrylamide gels. Nonetheless, when individual crystals used for X-ray diffraction were examined by SDS gel electrophoresis after data collection, two species of alpha chain were present, indicating that some proteolysis had occurred during the course of operations. Amino-terminal sequencing on post-X-ray crystals showed mostly intact native alpha- and gamma-chain sequences (the native beta chain is blocked). The overall structure differs from that of a native fibrinogen from chicken blood and those reported for a partially proteolyzed bovine fibrinogen in the nature of twist in the coiled-coil regions, likely due to weak forces imparted by unique crystal packing. As such, the structure adds to the inventory of possible conformations that may occur in solution. Other features include a novel interface with an antiparallel arrangement of beta chains and a unique tangential association of coiled coils from neighboring molecules. The carbohydrate groups attached to beta chains are unusually prominent, the full sweep of 11 sugar residues being positioned. As was the case for native chicken fibrinogen, no resolvable electron density could be associated with alphaC domains.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21440897 K.F.Schilke, and J.McGuire (2011).
Detection of nisin and fibrinogen adsorption on poly(ethylene oxide) coated polyurethane surfaces by time-of-flight secondary ion mass spectrometry (TOF-SIMS).
  J Colloid Interface Sci, 358, 14-24.  
21475196 P.Macheboeuf, C.Buffalo, C.Y.Fu, A.S.Zinkernagel, J.N.Cole, J.E.Johnson, V.Nizet, and P.Ghosh (2011).
Streptococcal M1 protein constructs a pathological host fibrinogen network.
  Nature, 472, 64-68.
PDB codes: 2xnx 2xny
21106983 T.Riedel, J.Suttnar, E.Brynda, M.Houska, L.Medved, and J.E.Dyr (2011).
Fibrinopeptides A and B release in the process of surface fibrin formation.
  Blood, 117, 1700-1706.  
21258685 V.M.Gun'ko, L.I.Mikhalovska, P.E.Tomlins, and S.V.Mikhalovsky (2011).
Competitive adsorption of macromolecules and real-time dynamics of Vroman-like effects.
  Phys Chem Chem Phys, 13, 4476-4485.  
20485772 M.Corno, A.Rimola, V.Bolis, and P.Ugliengo (2010).
Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules.
  Phys Chem Chem Phys, 12, 6309-6329.  
  20088938 W.Liu, C.R.Carlisle, E.A.Sparks, and M.Guthold (2010).
The mechanical properties of single fibrin fibers.
  J Thromb Haemost, 8, 1030-1036.  
19928926 G.Tsurupa, R.R.Hantgan, R.A.Burton, I.Pechik, N.Tjandra, and L.Medved (2009).
Structure, stability, and interaction of the fibrin(ogen) alphaC-domains.
  Biochemistry, 48, 12191-12201.  
  19718461 J.W.Weisel (2009).
Why dysfibrinogenaemias still matter.
  Thromb Haemost, 102, 426-427.  
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.