3GHG

Crystal Structure of Human Fibrinogen

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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


Literature

Crystal structure of human fibrinogen.

Kollman, J.M., Pandi, L., Sawaya, M.R., Riley, M., Doolittle, R.F.

(2009) Biochemistry 48: 3877-3886

  • DOI: 10.1021/bi802205g
  • Primary Citation of Related Structures:  
    3GHG

  • PubMed Abstract: 

    • A crystal structure of human fibrinogen has been determined at approximately 3.3 A resolution. The protein was purified from human blood plasma, first by a cold ethanol precipitation procedure and then by stepwise chromatography on DEAE-cellulose. A product was obtained that was homogeneous on SDS-polyacrylamide gels ...

    A crystal structure of human fibrinogen has been determined at approximately 3.3 A resolution. The protein was purified from human blood plasma, first by a cold ethanol precipitation procedure and then by stepwise chromatography on DEAE-cellulose. A product was obtained that was homogeneous on SDS-polyacrylamide gels. Nonetheless, when individual crystals used for X-ray diffraction were examined by SDS gel electrophoresis after data collection, two species of alpha chain were present, indicating that some proteolysis had occurred during the course of operations. Amino-terminal sequencing on post-X-ray crystals showed mostly intact native alpha- and gamma-chain sequences (the native beta chain is blocked). The overall structure differs from that of a native fibrinogen from chicken blood and those reported for a partially proteolyzed bovine fibrinogen in the nature of twist in the coiled-coil regions, likely due to weak forces imparted by unique crystal packing. As such, the structure adds to the inventory of possible conformations that may occur in solution. Other features include a novel interface with an antiparallel arrangement of beta chains and a unique tangential association of coiled coils from neighboring molecules. The carbohydrate groups attached to beta chains are unusually prominent, the full sweep of 11 sugar residues being positioned. As was the case for native chicken fibrinogen, no resolvable electron density could be associated with alphaC domains.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093-0314, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha chainA, D, G, J562Homo 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 
Entity Groups  
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UniProt GroupP02671
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chainB, E, H, K461Homo sapiensMutation(s): 0 
Gene Names: FGB
UniProt & NIH Common Fund Data Resources
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, F, I, L411Homo 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
A knobM, N, Q, R4N/AMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
B knobO, P, S, T4N/AMutation(s): 0 
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Oligosaccharides

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Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseU, V, X 11N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G79342RE
GlyCosmos:  G79342RE
GlyGen:  G79342RE
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseW 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G35461GE
GlyCosmos:  G35461GE
GlyGen:  G35461GE
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseY 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.238α = 90
b = 94.866β = 94.81
c = 300.812γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary