2A45

Crystal structure of the complex between thrombin and the central "E" region of fibrin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.290 
  • R-Value Observed: 0.221 

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Literature

Structural basis for sequential cleavage of fibrinopeptides upon fibrin assembly.

Pechik, I., Yakovlev, S., Mosesson, M.W., Gilliland, G.L., Medved, L.

(2006) Biochemistry 45: 3588-3597

  • DOI: 10.1021/bi0525369
  • Primary Citation of Related Structures:  
    2A45

  • PubMed Abstract: 

    • Nonsubstrate interaction of thrombin with fibrinogen promotes sequential cleavage of fibrinopeptides A and B (fpA and fpB, respectively) from the latter, resulting in its conversion into fibrin. The recently established crystal structure of human thrombin in complex with the central part of human fibrin clarified the mechanism of this interaction ...

    Nonsubstrate interaction of thrombin with fibrinogen promotes sequential cleavage of fibrinopeptides A and B (fpA and fpB, respectively) from the latter, resulting in its conversion into fibrin. The recently established crystal structure of human thrombin in complex with the central part of human fibrin clarified the mechanism of this interaction. Here, we reveal new details of the structure and present the results of molecular modeling of the fpA- and fpB-containing portions of the Aalpha and Bbeta chains, not identified in the complex, in both fibrinogen and protofibrils. The analysis of the results reveals that in fibrinogen the fpA-containing portions are in a more favorable position to bind in the active site cleft of bound thrombin. Surface plasmon resonance experiments establish that the fpB-containing portions interact with the fibrin-derived dimeric D-D fragment, suggesting that in protofibrils they bind to the newly formed DD regions bringing fpB into the vicinity of bound thrombin. These findings provide a coherent rationale for the preferential removal of fpA from fibrinogen at the first stage of fibrin assembly and the accelerated cleavage of fpB from protofibrils and/or fibrils at the second stage.

    Related Citations: 
    • Crystal Structure of the Complex between Thrombin and the Central "E" Region of Fibrin
      Pechik, I., Madrazo, J., Mosesson, M.W., Hernandez, I., Gilliland, G.L., Medved, L.
      (2004) Proc Natl Acad Sci U S A 101: 2718
    Organizational Affiliation: 

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and National Institute of Standards and Technology, Rockville, Maryland 20850, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA,
C [auth D]		36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainB,
D [auth E]		259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha chainE [auth G],
H [auth J]		57Homo sapiensMutation(s): 0 
Gene Names: FGA
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PHAROS:  P02671
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UniProt GroupP02671
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chainF [auth H],
I [auth K]		91Homo sapiensMutation(s): 0 
Gene Names: FGB
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PHAROS:  P02675
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UniProt GroupP02675
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chainG [auth I],
J [auth L]		45Homo sapiensMutation(s): 0 
Gene Names: FGG, PRO2061
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Find proteins for P02679 (Homo sapiens)
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PHAROS:  P02679
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6
Download Ideal Coordinates CCD File 
K [auth B],
M [auth E]		D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
L [auth B],
N [auth E]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020		K [auth B],
M [auth E]		D-Phe-Pro-Arg-CH2ClPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.290 
  • R-Value Observed: 0.221 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.263α = 90
b = 76.263β = 90
c = 192.452γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
CNSrefinement
SHELXL-97refinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2019-08-14
    Changes: Data collection, Refinement description