1RE4

Crystal Structure of Fragment D of BbetaD398A Fibrinogen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

BbetaGlu397 and BbetaAsp398 but not BbetaAsp432 are required for "B:b" interactions.

Kostelansky, M.S.Bolliger-Stucki, B.Betts, L.Gorkun, O.V.Lord, S.T.

(2004) Biochemistry 43: 2465-2474

  • DOI: 10.1021/bi035996f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerizatio ...

    We synthesized three fibrinogen variants, BbetaE397A, BbetaD398A, and BbetaD432A, with substitutions at positions identified in crystallographic studies as critical for binding the "B" peptide, Gly-His-Arg-Pro-amide (GHRPam), to the "b" polymerization site. We examined thrombin- and batroxobin-catalyzed polymerization by turbidity measurements and found that BbetaE397A and BbetaD398A were impaired while BbetaD432A was normal. Changes in polymerization as a function of calcium were similar for variant and normal fibrinogens. We determined crystal structures of fragment D from the variant BbetaD398A in the absence and presence of GHRPam. In the absence of peptide, the structure showed that the alanine substitution altered only specific local interactions, as alignment of the variant structure with the analogous normal structure resulted in an RMSD of 0.53 A over all atoms. The structure also showed reduced occupancy of the beta2 calcium-binding site that includes the side chain carbonyl of BbetaD398, suggesting that calcium was not bound at this site in our polymerization studies. In the presence of peptide, the structure showed that GHRPam was not bound in the "b" site and the conformational changes associated with peptide binding to normal fragment D did not occur. This structure also showed GHRPam bound in the "a" polymerization site, although in two different conformations. Calcium binding was associated with only one of these conformations, suggesting that calcium binding to the gamma2-site and an alternative peptide conformation were induced by crystal packing. We conclude that BbetaE397 and BbetaD398 are essential for the "B:b" interaction, while BbetaD432 is not.


    Organizational Affiliation

    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-7525, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen alpha/alpha-E chain
A, D
66Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Go to Gene View: FGA
Go to UniProtKB:  P02671
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chain
B, E
313Homo sapiensMutation(s): 1 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen gamma chain
C, F
311Homo sapiensMutation(s): 0 
Gene Names: FGG
Find proteins for P02679 (Homo sapiens)
Go to Gene View: FGG
Go to UniProtKB:  P02679
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.538α = 90.00
b = 94.487β = 90.00
c = 227.088γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-25
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance