4WUU

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.jmb.2015.12.002
  • Primary Citation of Related Structures:  
    4WUU

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain296Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P19544 (Homo sapiens)
Explore P19544 
Go to UniProtKB:  P19544
PHAROS:  P19544
GTEx:  ENSG00000184937 
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UniProt GroupP19544
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ESK1216Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN HEAVY CHAIN223Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.08α = 90
b = 118.26β = 90
c = 126.302γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-10-23
    Changes: Structure summary