1LTJ

Crystal Structure of Recombinant Human Fibrinogen Fragment D with the Peptide Ligands Gly-Pro-Arg-Pro-Amide and Gly-His-Arg-Pro-Amide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 

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This is version 2.0 of the entry. See complete history. 


Literature

2.8 A Crystal Structures of Recombinant Fibrinogen Fragment D with and without Two Peptide Ligands: GHRP Binding to the "b" Site Disrupts Its Nearby Calcium-binding Site.

Kostelansky, M.S., Betts, L., Gorkun, O.V., Lord, S.T.

(2002) Biochemistry 41: 12124-12132

  • DOI: 10.1021/bi0261894
  • Primary Citation of Related Structures:  
    1LT9, 1LTJ

  • PubMed Abstract: 

    • We report two crystal structures, each at a resolution of 2.8 A, of recombinant human fibrinogen fragment D (rfD) in the absence and presence of peptide ligands. The bound ligands, Gly-Pro-Arg-Pro-amide and Gly-His-Arg-Pro-amide, mimic the interactions of the thrombin exposed polymerization sites, "A" and "B", respectively ...

    We report two crystal structures, each at a resolution of 2.8 A, of recombinant human fibrinogen fragment D (rfD) in the absence and presence of peptide ligands. The bound ligands, Gly-Pro-Arg-Pro-amide and Gly-His-Arg-Pro-amide, mimic the interactions of the thrombin exposed polymerization sites, "A" and "B", respectively. This report is the first to describe the structure of fragment D in the presence of both peptide ligands. The structures reveal that recombinant fibrinogen is nearly identical to the plasma protein but with minor changes, like the addition of a proximal fucose to the carbohydrate linked to residue betaGln364, and slightly different relative positions of the beta- and gamma-modules. Of major interest in our structures is that a previously identified calcium site in plasma fibrinogen is absent when Gly-His-Arg-Pro-amide is bound. The peptide-dependent loss of this calcium site may have significant biological implications that are further discussed. These structures provide a foundation for the detailed structural analysis of variant recombinant fibrinogens that were used to identify critical functional residues within fragment D.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha/alpha-E chainA, D66Homo sapiensMutation(s): 0 
Gene Names: FGA
UniProt & NIH Common Fund Data Resources
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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, E313Homo 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, F311Homo sapiensMutation(s): 0 
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
Gly-Pro-Arg-ProG, I4N/AMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Gly-His-Arg-ProH, J4N/AMutation(s): 0 
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Oligosaccharides

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Entity ID: 6
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: 2.80 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.284α = 90
b = 94.218β = 90
c = 226.936γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-06
    Type: Initial release
  • Version 1.1: 2008-04-28
    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