3FIB

RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN RESIDUES K338 AND C339


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The primary fibrin polymerization pocket: three-dimensional structure of a 30-kDa C-terminal gamma chain fragment complexed with the peptide Gly-Pro-Arg-Pro.

Pratt, K.P.Cote, H.C.Chung, D.W.Stenkamp, R.E.Davie, E.W.

(1997) Proc Natl Acad Sci U S A 94: 7176-7181

  • DOI: 10.1073/pnas.94.14.7176
  • Primary Citation of Related Structures:  
    2FIB, 3FIB

  • PubMed Abstract: 
  • After vascular injury, a cascade of serine protease activations leads to the conversion of the soluble fibrinogen molecule into fibrin. The fibrin monomers then polymerize spontaneously and noncovalently to form a fibrin gel. The primary interaction ...

    After vascular injury, a cascade of serine protease activations leads to the conversion of the soluble fibrinogen molecule into fibrin. The fibrin monomers then polymerize spontaneously and noncovalently to form a fibrin gel. The primary interaction of this polymerization reaction is between the newly exposed N-terminal Gly-Pro-Arg sequence of the alpha chain of one fibrin molecule and the C-terminal region of a gamma chain of an adjacent fibrin(ogen) molecule. In this report, the polymerization pocket has been identified by determining the crystal structure of a 30-kDa C-terminal fragment of the fibrin(ogen) gamma chain complexed with the peptide Gly-Pro-Arg-Pro. This peptide mimics the N terminus of the alpha chain of fibrin. The conformational change in the protein upon binding the peptide is subtle, with electrostatic interactions primarily mediating the association. This is consistent with biophysical experiments carried out over the last 50 years on this fundamental polymerization reaction.


    Related Citations: 
    • Crystal Structure of a 30 kDa C-Terminal Fragment from the Gamma Chain of Human Fibrinogen
      Yee, V.C., Pratt, K.P., Cote, H.Cf., Le Trong, I., Chung, D.W., Davie, E.W., Stenkamp, R.E., Teller, D.C.
      (1997) Structure 5: 125

    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. kpratt@u.washington.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOGEN GAMMA CHAIN RESIDUESA249Homo sapiensMutation(s): 0 
Gene Names: FGGPRO2061
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS  P02679
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.53α = 90
b = 68.42β = 105.36
c = 47.67γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance