7KGU | pdb_00007kgu

Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7KGU

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: 191.72 kDa 
  • Atom Count: 13,756 
  • Modeled Residue Count: 1,690 
  • Deposited Residue Count: 1,728 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light Chain, Fab fragment, IGGA,
C,
E,
H [auth L]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy Chain, Fab, IGG, FabB,
D,
F,
G [auth H]
218Homo sapiensMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTB

Query on BTB



Download:Ideal Coordinates CCD File
J [auth A]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
O [auth B],
P [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth D]
AB [auth L]
BA [auth D]
I [auth A]
KA [auth F]
AA [auth D],
AB [auth L],
BA [auth D],
I [auth A],
KA [auth F],
SA [auth H],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BB [auth L]
CA [auth D]
DA [auth D]
EA [auth D]
FA [auth D]
BB [auth L],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
IA [auth D],
JA [auth D],
K [auth A],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
NA [auth F],
OA [auth F],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
S [auth B],
T [auth B],
TA [auth H],
U [auth B],
UA [auth H],
V [auth B],
VA [auth H],
WA [auth H],
X [auth C],
XA [auth H],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GLY

Query on GLY



Download:Ideal Coordinates CCD File
ZA [auth L]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
YA [auth H]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
CB [auth L],
RA [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.462α = 90
b = 263.955β = 99.53
c = 91.237γ = 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 States--
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary