3BT1

Structure of urokinase receptor, urokinase and vitronectin complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes

Huai, Q., Zhou, A., Lin, L., Mazar, A.P., Parry, G.C., Callahan, J., Shaw, D.E., Furie, B., Furie, B.C., Huang, M.

(2008) Nat Struct Mol Biol 15: 422-423

  • DOI: https://doi.org/10.1038/nsmb.1404
  • Primary Citation of Related Structures:  
    3BT1, 3BT2

  • PubMed Abstract: 

    The urokinase receptor (uPAR) can recognize several ligands. The structural basis for this multiple ligand recognition by uPAR is unknown. This study reports the crystal structures of uPAR in complex with both urokinase (uPA) and vitronectin and reveal that uPA occupies the central cavity of the receptor, whereas vitronectin binds at the outer side of the receptor. These results provide a structural understanding of one receptor binding to two ligands.

    • Organizational Affiliation: 

    Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator135Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
GTEx:  ENSG00000122861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00749
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vitronectin40Homo sapiensMutation(s): 0 
Gene Names: VTN
UniProt & NIH Common Fund Data Resources
Find proteins for P04004 (Homo sapiens)
Explore P04004 
Go to UniProtKB:  P04004
PHAROS:  P04004
GTEx:  ENSG00000109072 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04004
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptorC [auth U]283Homo sapiensMutation(s): 0 
Gene Names: PLAUR, MO3, UPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q03405 (Homo sapiens)
Explore Q03405 
Go to UniProtKB:  Q03405
PHAROS:  Q03405
GTEx:  ENSG00000011422 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03405
Glycosylation
Glycosylation Sites: 3
Go to GlyGen: Q03405-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.353α = 90
b = 105.187β = 90
c = 55.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-03-25 
    • Deposition Author(s): Huang, M.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2019-12-11
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2019-12-18
    Changes: Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary