4K24

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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:  

  • 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 ...

    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

    Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activator
A
135Homo sapiensMutation(s): 0 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vitronectin
B
40Homo sapiensMutation(s): 0 
Gene Names: VTN
Find proteins for P04004 (Homo sapiens)
Go to Gene View: VTN
Go to UniProtKB:  P04004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
anti-uPAR antibody, heavy chain
H
228N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
anti-uPAR antibody, light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Urokinase plasminogen activator surface receptor
U
283Homo sapiensMutation(s): 0 
Gene Names: PLAUR (MO3, UPAR)
Find proteins for Q03405 (Homo sapiens)
Go to Gene View: PLAUR
Go to UniProtKB:  Q03405
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
U
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
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: 4.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 164.659α = 90.00
b = 164.659β = 90.00
c = 391.582γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Data collection