4K24

Structure of anti-uPAR Fab ATN-658 in complex with uPAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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Literature

Identification of a New Epitope in uPAR as a Target for the Cancer Therapeutic Monoclonal Antibody ATN-658, a Structural Homolog of the uPAR Binding Integrin CD11b ( alpha M)

Xu, X.Cai, Y.Wei, Y.Donate, F.Juarez, J.Parry, G.Chen, L.Meehan, E.J.Ahn, R.W.Ugolkov, A.Dubrovskyi, O.O'halloran, T.V.Huang, M.Mazar, A.P.

(2014) PLoS One 9: e85349-e85349

  • DOI: 10.1371/journal.pone.0085349
  • Primary Citation of Related Structures:  
    4K23, 4K24

  • PubMed Abstract: 
  • The urokinase plasminogen activator receptor (uPAR) plays a role in tumor progression and has been proposed as a target for the treatment of cancer. We recently described the development of a novel humanized monoclonal antibody that targets uPAR and has ...

    The urokinase plasminogen activator receptor (uPAR) plays a role in tumor progression and has been proposed as a target for the treatment of cancer. We recently described the development of a novel humanized monoclonal antibody that targets uPAR and has anti-tumor activity in multiple xenograft animal tumor models. This antibody, ATN-658, does not inhibit ligand binding (i.e. uPA and vitronectin) to uPAR and its mechanism of action remains unclear. As a first step in understanding the anti-tumor activity of ATN-658, we set out to identify the epitope on uPAR to which ATN-658 binds. Guided by comparisons between primate and human uPAR, epitope mapping studies were performed using several orthogonal techniques. Systematic site directed and alanine scanning mutagenesis identified the region of aa 268-275 of uPAR as the epitope for ATN-658. No known function has previously been attributed to this epitope Structural insights into epitope recognition were obtained from structural studies of the Fab fragment of ATN-658 bound to uPAR. The structure shows that the ATN-658 binds to the DIII domain of uPAR, close to the C-terminus of the receptor, corroborating the epitope mapping results. Intriguingly, when bound to uPAR, the complementarity determining region (CDR) regions of ATN-658 closely mimic the binding regions of the integrin CD11b (αM), a previously identified uPAR ligand thought to be involved in leukocyte rolling, migration and complement fixation with no known role in tumor progression of solid tumors. These studies reveal a new functional epitope on uPAR involved in tumor progression and demonstrate a previously unrecognized strategy for the therapeutic targeting of uPAR.


    Organizational Affiliation

    Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, United States of America ; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois, United States of America ; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator A135Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
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Go to UniProtKB:  P00749
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PHAROS:  P00749
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Vitronectin B40Homo sapiensMutation(s): 0 
Gene Names: VTN
Find proteins for P04004 (Homo sapiens)
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PHAROS:  P04004
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, heavy chain H228Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
anti-uPAR antibody, light chain L219Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase plasminogen activator surface receptor U283Homo sapiensMutation(s): 0 
Gene Names: MO3PLAURUPAR
Find proteins for Q03405 (Homo sapiens)
Explore Q03405 
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PHAROS:  Q03405
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
U
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
U
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.659α = 90
b = 164.659β = 90
c = 391.582γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Data collection
  • Version 1.2: 2019-12-11
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary