1DEQ

THE CRYSTAL STRUCTURE OF MODIFIED BOVINE FIBRINOGEN (AT ~4 ANGSTROM RESOLUTION)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of modified bovine fibrinogen.

Brown, J.H.Volkmann, N.Jun, G.Henschen-Edman, A.H.Cohen, C.

(2000) Proc.Natl.Acad.Sci.USA 97: 85-90


  • PubMed Abstract: 
  • Here we report the crystal structure at approximately 4-A resolution of a selectively proteolyzed bovine fibrinogen. This key component in hemostasis is an elongated 340-kDa glycoprotein in the plasma that upon activation by thrombin self-assembles t ...

    Here we report the crystal structure at approximately 4-A resolution of a selectively proteolyzed bovine fibrinogen. This key component in hemostasis is an elongated 340-kDa glycoprotein in the plasma that upon activation by thrombin self-assembles to form the fibrin clot. The crystals are unusual because they are made up of end-to-end bonded molecules that form flexible filaments. We have visualized the entire coiled-coil region of the molecule, which has a planar sigmoidal shape. The primary polymerization receptor pockets at the ends of the molecule face the same way throughout the end-to-end bonded filaments, and based on this conformation, we have developed an improved model of the two-stranded protofibril that is the basic building block in fibrin. Near the middle of the coiled-coil region, the plasmin-sensitive segment is a hinge about which the molecule adopts different conformations. This segment also includes the boundary between the three- and four-stranded portions of the coiled coil, indicating the location on the backbone that anchors the extended flexible Aalpha arm. We suggest that a flexible branch point in the molecule may help accommodate variability in the structure of the fibrin clot.


    Related Citations: 
    • Fibrinogen Structure in Projection at 18 Angstroms Resolution
      Rao, S.P.S.,Poojary, M.D.,Elliott Jr., B.W.,Melanson, L.A.,Oriel, B.,Cohen, C.
      (1991) J.Mol.Biol. 222: 89
    • Crystalline States of a Modified Fibrinogen
      Tooney, N.M.,Cohen, C.
      (1977) J.Mol.Biol. 110: 363
    • Crystals of Modified Fibrinogen: Size, Shape and Packing of Molecules
      Weisel, J.W.,Warren, S.G.,Cohen, C.
      (1978) J.Mol.Biol. 126: 159


    Organizational Affiliation

    Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN (ALPHA CHAIN)
A, D, N, Q
390Bos taurusGene Names: FGA
Find proteins for P02672 (Bos taurus)
Go to Gene View: FGA
Go to UniProtKB:  P02672
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN (BETA CHAIN)
B, E, O, R
408Bos taurusGene Names: FGB
Find proteins for P02676 (Bos taurus)
Go to Gene View: FGB
Go to UniProtKB:  P02676
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN (GAMMA CHAIN)
C, F, P, S
411Bos taurusGene Names: FGG
Find proteins for P12799 (Bos taurus)
Go to Gene View: FGG
Go to UniProtKB:  P12799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
M, Z
90N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
M, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 176.006α = 90.00
b = 94.935β = 94.41
c = 209.805γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance