1DEQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 U S A 97: 85-90

  • DOI: https://doi.org/10.1073/pnas.97.1.85
  • Primary Citation of Related Structures:  
    1DEQ

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN (ALPHA CHAIN)A,
D,
H [auth N],
K [auth Q]
390Bos taurusMutation(s): 0 
UniProt
Find proteins for P02672 (Bos taurus)
Explore P02672 
Go to UniProtKB:  P02672
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02672
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN (BETA CHAIN)B,
E,
I [auth O],
L [auth R]
408Bos taurusMutation(s): 0 
UniProt
Find proteins for P02676 (Bos taurus)
Explore P02676 
Go to UniProtKB:  P02676
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02676
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGEN (GAMMA CHAIN)C,
F,
J [auth P],
M [auth S]
411Bos taurusMutation(s): 0 
UniProt
Find proteins for P12799 (Bos taurus)
Explore P12799 
Go to UniProtKB:  P12799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12799
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
FIBRINOGENG [auth M],
N [auth Z]
90Bos taurusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.006α = 90
b = 94.935β = 94.41
c = 209.805γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-09
    Changes: Data collection, Database references, Refinement description