6UJ9

Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens.

Hwang, M.S.Miller, M.S.Thirawatananond, P.Douglass, J.Wright, K.M.Hsiue, E.H.Mog, B.J.Aytenfisu, T.Y.Murphy, M.B.Aitana Azurmendi, P.Skora, A.D.Pearlman, A.H.Paul, S.DiNapoli, S.R.Konig, M.F.Bettegowda, C.Pardoll, D.M.Papadopoulos, N.Kinzler, K.W.Vogelstein, B.Zhou, S.Gabelli, S.B.

(2021) Nat Commun 12: 5271-5271

  • DOI: https://doi.org/10.1038/s41467-021-25605-4
  • Primary Citation of Related Structures:  
    6UJ7, 6UJ8, 6UJ9, 7KGU

  • PubMed Abstract: 

    Chimeric antigen receptor (CAR) T cells have emerged as a promising class of therapeutic agents, generating remarkable responses in the clinic for a subset of human cancers. One major challenge precluding the wider implementation of CAR therapy is the paucity of tumor-specific antigens. Here, we describe the development of a CAR targeting the tumor-specific isocitrate dehydrogenase 2 (IDH2) with R140Q mutation presented on the cell surface in complex with a common human leukocyte antigen allele, HLA-B*07:02. Engineering of the hinge domain of the CAR, as well as crystal structure-guided optimization of the IDH2 R140Q -HLA-B*07:02-targeting moiety, enhances the sensitivity and specificity of CARs to enable targeting of this HLA-restricted neoantigen. This approach thus holds promise for the development and optimization of immunotherapies specific to other cancer driver mutations that are difficult to target by conventional means.


  • Organizational Affiliation

    Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chain298Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
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UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin119Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
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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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP], mitochondrial10Homo sapiensMutation(s): 1 
EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for P48735 (Homo sapiens)
Explore P48735 
Go to UniProtKB:  P48735
PHAROS:  P48735
GTEx:  ENSG00000182054 
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UniProt GroupP48735
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainD [auth L]214Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainE [auth H]218Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE

Download Ideal Coordinates CCD File 
I [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
O [auth B]
Q [auth L]
F [auth A],
G [auth A],
H [auth A],
O [auth B],
Q [auth L],
R [auth L]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth B],
S [auth H],
T [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.605α = 90
b = 42.006β = 92.75
c = 125.18γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesCDMRP BC151831
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA062924
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA006973

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description