3E1I

Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand Gly-His-Arg-Pro-amide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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This is version 1.5 of the entry. See complete history


Literature

Fibrinogen variant BbetaD432A has normal polymerization but does not bind knob "B".

Bowley, S.R.Lord, S.T.

(2009) Blood 113: 4425-4430

  • DOI: https://doi.org/10.1182/blood-2008-09-178178
  • Primary Citation of Related Structures:  
    3E1I

  • PubMed Abstract: 
  • Fibrinogen residue Bbeta432Asp is part of hole "b" that interacts with knob "B," whose sequence starts with Gly-His-Arg-Pro-amide (GHRP). Because previous studies showed BbetaD432A has normal polymerization, we hypothesized that Bbeta432Asp is not critical for knob "B" binding and that new knob-hole interactions would compensate for the loss of this Asp residue ...

    Fibrinogen residue Bbeta432Asp is part of hole "b" that interacts with knob "B," whose sequence starts with Gly-His-Arg-Pro-amide (GHRP). Because previous studies showed BbetaD432A has normal polymerization, we hypothesized that Bbeta432Asp is not critical for knob "B" binding and that new knob-hole interactions would compensate for the loss of this Asp residue. To test this hypothesis, we solved the crystal structure of fragment D from BbetaD432A. Surprisingly, the structure (rfD-BbetaD432A+GH) showed the peptide GHRP was not bound to hole "b." We then re-evaluated the polymerization of this variant by examining clot turbidity, clot structure, and the rate of FXIIIa cross-linking. The turbidity and the rate of gamma-gamma dimer formation for BbetaD432A were indistinguishable compared with normal fibrinogen. Scanning electron microscopy showed no significant differences between the clots of BbetaD432A and normal, but the thrombin-derived clots had thicker fibers than clots obtained from batroxobin, suggesting that cleavage of FpB is more important than "B:b" interactions. We conclude that hole "b" and "B:b" knob-hole binding per se have no influence on fibrin polymerization.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha chainA, D87Homo sapiensMutation(s): 0 
Gene Names: FGA
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Go to UniProtKB:  P02671
PHAROS:  P02671
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UniProt GroupP02671
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chainB, E328Homo sapiensMutation(s): 1 
Gene Names: FGB
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Find proteins for P02675 (Homo sapiens)
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PHAROS:  P02675
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UniProt GroupP02675
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chainC, F319Homo sapiensMutation(s): 0 
Gene Names: FGGPRO2061
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Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
PHAROS:  P02679
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UniProt GroupP02679
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Gly-His-Arg-Pro-amideG, H5synthetic constructMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.476α = 90
b = 146.596β = 90
c = 228.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2013-09-18
    Changes: Derived calculations
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.5: 2021-10-20
    Changes: Database references, Structure summary