7V63

Structure of dimeric uPAR at low pH

• PDB DOI: https://doi.org/10.2210/pdb7V63/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2021-08-19 Released: 2021-12-22 
• Deposition Author(s): Yuan, C., Huang, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 

Literature

Crystal structure and cellular functions of uPAR dimer

Yu, S., Sui, Y., Wang, J., Li, Y., Li, H., Cao, Y., Chen, L., Jiang, L., Yuan, C., Huang, M.

(2022) Nat Commun 13: 1665

• DOI: https://doi.org/10.1038/s41467-022-29344-y

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.77 kDa 
• Atom Count: 2,833 
• Modelled Residue Count: 371 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator surface receptor	A, B	279	Homo sapiens	Mutation(s): 0  Gene Names: UPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q03405 (Homo sapiens) Explore Q03405  Go to UniProtKB:  Q03405
PHAROS:  Q03405 GTEx:  ENSG00000011422

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.449	α = 90
b = 77.449	β = 90
c = 275.526	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CRANK	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Yuan, C., Huang, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077016, 82070142, 31570745, 31670739

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2022-04-06
  Changes: Database references