1JY3

Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the central region of bovine fibrinogen (E5 fragment) at 1.4-A resolution.

Madrazo, J.Brown, J.H.Litvinovich, S.Dominguez, R.Yakovlev, S.Medved, L.Cohen, C.

(2001) Proc.Natl.Acad.Sci.USA 98: 11967-11972

  • DOI: 10.1073/pnas.211439798
  • Primary Citation of Related Structures:  1JY2

  • PubMed Abstract: 
  • The high-resolution crystal structure of the N-terminal central region of bovine fibrinogen (a 35-kDa E(5) fragment) reveals a remarkable dimeric design. The two halves of the molecule bond together at the center in an extensive molecular "handshake" ...

    The high-resolution crystal structure of the N-terminal central region of bovine fibrinogen (a 35-kDa E(5) fragment) reveals a remarkable dimeric design. The two halves of the molecule bond together at the center in an extensive molecular "handshake" by using both disulfide linkages and noncovalent contacts. On one face of the fragment, the Aalpha and Bbeta chains from the two monomers form a funnel-shaped domain with an unusual hydrophobic cavity; here, on each of the two outer sides there appears to be a binding site for thrombin. On the opposite face, the N-terminal gamma chains fold into a separate domain. Despite the chemical identity of the two halves of fibrinogen, an unusual pair of adjacent disulfide bonds locally constrain the two gamma chains to adopt different conformations. The striking asymmetry of this domain may promote the known supercoiling of the protofibrils in fibrin. This information on the detailed topology of the E(5) fragment permits the construction of a more detailed model than previously possible for the critical trimolecular junction of the protofibril in fibrin.


    Related Citations: 
    • 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


    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
N, Q
53Bos 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
O, R
56Bos 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-B CHAIN
P, S
48Bos taurusGene Names: FGG
Find proteins for P12799 (Bos taurus)
Go to Gene View: FGG
Go to UniProtKB:  P12799
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.700α = 90.00
b = 59.100β = 90.00
c = 97.300γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
ARPmodel building
DENZOdata reduction
CNSrefinement
DMphasing
DMmodel building
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description