1RF1

Crystal Structure of Fragment D of gammaE132A Fibrinogen with the Peptide Ligand Gly-His-Arg-Pro-amide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report



Literature

Calcium-Binding Site beta2, Adjacent to the "b" Polymerization Site, Modulates Lateral Aggregation of Protofibrils during Fibrin Polymerization.

Kostelansky, M.S., Lounes, K.C., Ping, L.F., Dickerson, S.K., Gorkun, O.V., Lord, S.T.

(2004) Biochemistry 43: 2475-2483

  • DOI: 10.1021/bi0359978
  • Primary Citation of Related Structures:  
    1RF1, 1RF0

  • PubMed Abstract: 

    • Structural analysis of recombinant fibrinogen fragment D revealed that the calcium-binding site (beta2-site) composed of residues BbetaAsp261, BbetaAsp398, BbetaGly263, and gammaGlu132 is modulated by the "B:b" interaction. To determine the beta2-site's ...

    Structural analysis of recombinant fibrinogen fragment D revealed that the calcium-binding site (beta2-site) composed of residues BbetaAsp261, BbetaAsp398, BbetaGly263, and gammaGlu132 is modulated by the "B:b" interaction. To determine the beta2-site's role in polymerization, we engineered variant fibrinogen gammaE132A in which calcium binding to the beta2-site was disrupted by replacing glutamic acid at gamma132 with alanine. We compared polymerization of gammaE132A to normal fibrinogen as a function of calcium concentration. Polymerization of gammaE132A at concentrations of calcium

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha/alpha-E chain A, D66Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Explore P02671 
Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS:  P02671
GTEx:  ENSG00000171560
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chain B, E313Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Explore P02675 
Go to UniProtKB:  P02675
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PHAROS:  P02675
GTEx:  ENSG00000171564
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chain C, F311Homo sapiensMutation(s): 1 
Gene Names: FGG, PRO2061
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS:  P02679
GTEx:  ENSG00000171557
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
GHRP peptide G, H, I, J4N/AMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
K, L
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.714α = 90
b = 94.683β = 90
c = 228.198γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary