4WUU

Structure of ESK1 in complex with HLA-A*0201/WT1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.047 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of a TCR-Mimic Antibody with Target Predicts Pharmacogenetics.

Ataie, N., Xiang, J., Cheng, N., Brea, E.J., Lu, W., Scheinberg, D.A., Liu, C., Ng, H.L.

(2016) J.Mol.Biol. 428: 194-205

  • DOI: 10.1016/j.jmb.2015.12.002

  • PubMed Abstract: 

    • Antibody therapies currently target only extracellular antigens. A strategy to recognize intracellular antigens is to target peptides presented by immune HLA receptors. ESK1 is a human, T-cell receptor (TCR)-mimic antibody that binds with subnanomola ...

    Antibody therapies currently target only extracellular antigens. A strategy to recognize intracellular antigens is to target peptides presented by immune HLA receptors. ESK1 is a human, T-cell receptor (TCR)-mimic antibody that binds with subnanomolar affinity to the RMF peptide from the intracellular Wilms tumor oncoprotein WT1 in complex with HLA-A*02:01. ESK1 is therapeutically effective in mouse models of WT1(+) human cancers. TCR-based therapies have been presumed to be restricted to one HLA subtype. The mechanism for the specificity and high affinity of ESK1 is unknown. We show in a crystal structure that ESK1 Fab binds to RMF/HLA-A*02:01 in a mode different from that of TCRs. From the structure, we predict and then experimentally confirm high-affinity binding with multiple other HLA-A*02 subtypes, broadening the potential patient pool for ESK1 therapy. Using the crystal structure, we also predict potential off-target binding that we experimentally confirm. Our results demonstrate how protein structure information can contribute to personalized immunotherapy.

    Organizational Affiliation: 

    University of Hawaii at Manoa, Department of Chemistry, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
296Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01892
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
C
9Homo sapiensMutation(s): 0 
Gene Names: WT1
Find proteins for P19544 (Homo sapiens)
Go to Gene View: WT1
Go to UniProtKB:  P19544
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ESK1
D
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN HEAVY CHAIN
E
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.047 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.080α = 90.00
b = 118.260β = 90.00
c = 126.302γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2014-11-03 
  • Released Date: 2015-12-30 
  • Deposition Author(s): Ataie, N.J., Ng, H.L.

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-10
    Type: Database references