6AEX

Crystal structure of unoccupied murine uPAR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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Literature

Crystal structure of the unoccupied murine urokinase-type plasminogen activator receptor (uPAR) reveals a tightly packed DII-DIII unit.

Liu, M., Lin, L., Hoyer-Hansen, G., Ploug, M., Li, H., Jiang, L., Yuan, C., Li, J., Huang, M.

(2019) FEBS Lett 593: 1236-1247

  • DOI: 10.1002/1873-3468.13397
  • Primary Citation of Related Structures:  
    6AEX

  • PubMed Abstract: 

    • The urokinase-type plasminogen activator receptor (uPAR) is a cell surface receptor that is capable of binding to a range of extracellular proteins and triggering a series of proteolytic and signaling events. Previous structural studies of uPAR with its ligands uPA and vitronectin revealed that its three domains (DI, DII, and DIII) form a large hydrophobic cavity to accommodate uPA ...

    The urokinase-type plasminogen activator receptor (uPAR) is a cell surface receptor that is capable of binding to a range of extracellular proteins and triggering a series of proteolytic and signaling events. Previous structural studies of uPAR with its ligands uPA and vitronectin revealed that its three domains (DI, DII, and DIII) form a large hydrophobic cavity to accommodate uPA. In the present study, the structure of unoccupied murine uPAR (muPAR) is determined. The structure of DII and DIII of muPAR is well defined and forms a compact globular unit, while DI could not be traced. Molecular dynamic simulations further confirm the rigid binding interface between DII and DIII. This study shows overall structural flexibility of uPAR in the absence of uPA.

    Organizational Affiliation: 

    College of Chemistry, Fuzhou University, China.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptorA [auth U]277Mus musculusMutation(s): 0 
Gene Names: Plaur
UniProt & NIH Common Fund Data Resources
Find proteins for P35456 (Mus musculus)
Explore P35456 
Go to UniProtKB:  P35456
IMPC:  MGI:97612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35456
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
B [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: 2.39 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.82α = 90
b = 83.82β = 90
c = 81.398γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370737
National Natural Science Foundation of ChinaChina31400637
National Natural Science Foundation of ChinaChina31570745
National Natural Science Foundation of ChinaChina31670739

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary