3BT2

Structure of urokinase receptor, urokinase and vitronectin complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

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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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator135Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
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PHAROS:  P00749
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UniProt GroupP00749
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vitronectin40Homo sapiensMutation(s): 0 
Gene Names: VTN
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Find proteins for P04004 (Homo sapiens)
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PHAROS:  P04004
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UniProt GroupP04004
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, light chainC [auth L]212Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, heavy chainD [auth H]214Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptorE [auth U]283Homo sapiensMutation(s): 0 
Gene Names: PLAUR, MO3, UPAR
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Find proteins for Q03405 (Homo sapiens)
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PHAROS:  Q03405
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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)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth C],
G [auth D]		2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
H [auth U]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.096α = 90
b = 87.205β = 94.31
c = 124.274γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
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: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary