3BVH

Crystal Structure of Recombinant gammaD364A Fibrinogen Fragment D with the Peptide Ligand Gly-Pro-Arg-Pro-Amide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Polymerization-defective fibrinogen variant gammaD364A binds knob "A" peptide mimic.

Bowley, S.R., Merenbloom, B.K., Okumura, N., Betts, L., Heroux, A., Gorkun, O.V., Lord, S.T.

(2008) Biochemistry 47: 8607-8613

  • DOI: 10.1021/bi8000769
  • Primary Citation of Related Structures:  
    3BVH

  • PubMed Abstract: 

    • Fibrin polymerization is supported in part by interactions called "A:a". Crystallographic studies revealed gamma364Asp is part of hole "a" that interacts with knob "A" peptide mimic, GPRP. Biochemical studies have shown gamma364Asp is critical to polymerization, as polymerization of variants gammaD364A, gammaD364H, and gammaD364V is exceptionally impaired ...

    Fibrin polymerization is supported in part by interactions called "A:a". Crystallographic studies revealed gamma364Asp is part of hole "a" that interacts with knob "A" peptide mimic, GPRP. Biochemical studies have shown gamma364Asp is critical to polymerization, as polymerization of variants gammaD364A, gammaD364H, and gammaD364V is exceptionally impaired. To understand the molecular basis for the aberrant function, we solved the crystal structure of fragment D from gammaD364A. Surprisingly, the structure (rfD-gammaD364A+GP) showed near normal "A:a" interactions with GPRP bound to hole "a" and no change in the overall structure of gammaD364A. Of note, inspection of the structure showed negative electrostatic potential inside hole "a" was diminished by this substitution. We examined GPRP binding to the gamma364Asp variants in solution by plasmin protection assay. We found no protection of either gammaD364H or gammaD364V but partial protection of gammaD364A, indicating the peptide does not bind to either gammaD364H or gammaD364V and binds more weakly than normal to gammaD364A. We also examined protection by calcium and found all variants were indistinguishable from normal, suggesting the global structures of the variants are not markedly different from normal. Our data imply that gamma364Asp per se is not required for knob "A" binding to hole "a"; rather, this residue's negative charge has a critical role in the electrostatic interactions that facilitate the important first step in fibrin polymerization.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha chainA, D62Homo sapiensMutation(s): 0 
Gene Names: FGA
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens)
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Go to UniProtKB:  P02671
PHAROS:  P02671
GTEx:  ENSG00000171560 
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UniProt GroupP02671
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chainB, E298Homo sapiensMutation(s): 0 
Gene Names: FGB
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Find proteins for P02675 (Homo sapiens)
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Go to UniProtKB:  P02675
PHAROS:  P02675
GTEx:  ENSG00000171564 
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UniProt GroupP02675
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chainC, F293Homo sapiensMutation(s): 1 
Gene Names: FGG, PRO2061
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
PHAROS:  P02679
GTEx:  ENSG00000171557 
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UniProt GroupP02679
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
4-mer peptide GPRPG,
I [auth H],
H [auth I],
J		4synthetic constructMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseK, L 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.844α = 90
b = 94.913β = 90
c = 225.754γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2018-12-26
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary