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 

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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
  • 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 af ...

    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; University of Hawaii Cancer Center, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA. Electronic address: hng@hawaii.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain A296Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS:  P04439
GTEx:  ENSG00000206503
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulin B100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS:  P61769
GTEx:  ENSG00000166710
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU C9Homo sapiensMutation(s): 0 
Gene Names: WT1
Find proteins for P19544 (Homo sapiens)
Explore P19544 
Go to UniProtKB:  P19544
NIH Common Fund Data Resources
PHAROS:  P19544
GTEx:  ENSG00000184937
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ESK1 D216Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN HEAVY CHAIN E223Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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

  • 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
    Changes: Database references