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 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


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
  • Structures With Same Primary Citation

  • 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 thr ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
A, D
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
B, E
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen alpha chain
G, J
57Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS  P02671
Protein Feature View
  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen gamma chain
I, L
45Homo sapiensMutation(s): 0 
Gene Names: FGGPRO2061
Find proteins for P02679 (Homo sapiens)
Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS  P02679
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chain
H, K
91Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to UniProtKB:  P02675
NIH Common Fund Data Resources
PHAROS  P02675
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download CCD File 
B, 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 CCD File 
B, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
B, ED-Phe-Pro-Arg-CH2ClPeptide-like /  Inhibitor

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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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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