4QTI

Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Stabilizing a flexible interdomain hinge region harboring the SMB binding site drives uPAR into its closed conformation.

Zhao, B.Gandhi, S.Yuan, C.Luo, Z.Li, R.Gardsvoll, H.de Lorenzi, V.Sidenius, N.Huang, M.Ploug, M.

(2015) J Mol Biol 427: 1389-1403

  • DOI: 10.1016/j.jmb.2015.01.022
  • Primary Citation of Related Structures:  
    4QTH, 4QTI

  • PubMed Abstract: 
  • The urokinase-type plasminogen activator receptor (uPAR) is a multidomain glycolipid-anchored membrane protein, which facilitates extracellular matrix remodeling by focalizing plasminogen activation to cell surfaces via its high-affinity interaction with uPA ...

    The urokinase-type plasminogen activator receptor (uPAR) is a multidomain glycolipid-anchored membrane protein, which facilitates extracellular matrix remodeling by focalizing plasminogen activation to cell surfaces via its high-affinity interaction with uPA. The modular assembly of its three LU (Ly6/uPAR-like) domains is inherently flexible and binding of uPA drives uPAR into its closed conformation, which presents the higher-affinity state for vitronectin thus providing an allosteric regulatory mechanism. Using a new class of epitope-mapped anti-uPAR monoclonal antibodies (mAbs), we now demonstrate that the reciprocal stabilization is indeed also possible. By surface plasmon resonance studies, we show that these mAbs and vitronectin have overlapping binding sites on uPAR and that they share Arg91 as hotspot residue in their binding interfaces. The crystal structure solved for one of these uPAR·mAb complexes at 3.0Å clearly shows that this mAb preselects the closed uPAR conformation with an empty but correctly assembled large hydrophobic binding cavity for uPA. Accordingly, these mAbs inhibit the uPAR-dependent lamellipodia formation and migration on vitronectin-coated matrices irrespective of the conformational status of uPAR and its occupancy with uPA. This is the first study to the best of our knowledge, showing that the dynamic assembly of the three LU domains in uPARwt can be driven toward the closed form by an external ligand, which is not engaging the hydrophobic uPA binding cavity. As this binding interface is also exploited by the somatomedin B domain of vitronectin, therefore, this relationship should be taken into consideration when exploring uPAR-dependent cell adhesion and migration in vitronectin-rich environments.


    Organizational Affiliation

    Finsen Laboratory, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen North, Denmark; Biotech Research and Innovation Centre, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen North, Denmark; Danish-Chinese Centre for Proteases and Cancer. Electronic address: m-ploug@finsenlab.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, heavy chainA [auth H]224Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, light chainB [auth L]214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptorC [auth U]283Homo sapiensMutation(s): 0 
Gene Names: PLAURMO3UPAR
UniProt & NIH Common Fund Data Resources
Find proteins for Q03405 (Homo sapiens)
Explore Q03405 
Go to UniProtKB:  Q03405
PHAROS:  Q03405
Entity Groups  
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UniProt GroupQ03405
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.554α = 90
b = 95.403β = 90
c = 189.533γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references