6AEX

Crystal structure of unoccupied murine uPAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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 ...

    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

    Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Biotechnology Research Innovation Centre (BRIC), University of Copenhagen, Denmark.,College of Life Science, Fujian Normal University, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, China.,Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark.,College of Chemistry, Fuzhou University, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase plasminogen activator surface receptor
U
277Mus musculusMutation(s): 0 
Gene Names: Plaur
Find proteins for P35456 (Mus musculus)
Go to UniProtKB:  P35456
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
U
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.393 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.820α = 90.00
b = 83.820β = 90.00
c = 81.398γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-06 
  • Released Date: 2019-07-17 
  • Deposition Author(s): Min, L., Huang, M.

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 

  • Version 1.0: 2019-07-17
    Type: Initial release