6UJ8 | pdb_00006uj8

Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.260 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UJ8

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 100.36 kDa 
  • Atom Count: 6,620 
  • Modeled Residue Count: 772 
  • Deposited Residue Count: 854 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chain
A, D
298Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
119Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP], mitochondrial
C, F
10Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48735
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
H [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
O [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
M [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]
I [auth A]
L [auth B]
N [auth B]
P [auth D]
G [auth A],
I [auth A],
L [auth B],
N [auth B],
P [auth D],
R [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
Q [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.260 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.69α = 90
b = 70.48β = 107.65
c = 88.146γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


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

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
  • Version 1.3: 2024-10-09
    Changes: Structure summary