Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.94 kDa 
• Atom Count: 6420 
• Residue Count: 818 
• Unique protein chains: 5

4WUU

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

• DOI: 10.2210/pdb4WUU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Cricetulus griseus
• Mutation(s): No 


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

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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 

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

• PubMed: 26688548 
• 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 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	296	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU	C	9	Homo sapiens	Mutation(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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ESK1	D	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN HEAVY CHAIN	E	223	Homo sapiens	Mutation(s): 0

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 = 70.08	α = 90
b = 118.26	β = 90
c = 126.302	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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