6AEX

Crystal structure of unoccupied murine uPAR

• PDB DOI: https://doi.org/10.2210/pdb6AEX/pdb

• Classification: CELL INVASION
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-08-06 Released: 2019-07-17 
• Deposition Author(s): Min, L., Huang, M.
• Funding Organization(s): National Natural Science Foundation of China

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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 

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

• PubMed: 31044429 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

College of Biological Science and Engineering, Fuzhou University, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 30.39 kDa 
• Atom Count: 1,261 
• Modelled Residue Count: 165 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator surface receptor	A [auth U]	277	Mus musculus	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	B [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 83.82	α = 90
b = 83.82	β = 90
c = 81.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370737
National Natural Science Foundation of China	China	31400637
National Natural Science Foundation of China	China	31570745
National Natural Science Foundation of China	China	31670739

Revision History  

• 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
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary