7OW6

Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK)

• PDB DOI: https://doi.org/10.2210/pdb7OW6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-16 Released: 2022-07-20 
• Deposition Author(s): Karuppiah, V., Robinson, R.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen

Poole, A., Karuppiah, V., Hartt, A., Haidar, J.N., Moureau, S., Dobrzycki, T., Hayes, C., Rowley, C., Dias, J., Harper, S., Barnbrook, K., Hock, M., Coles, C., Yang, W., Aleksic, M., Lin, A.B., Robinson, R., Dukes, J.D., Liddy, N., Van der Kamp, M., Plowman, G.D., Vuidepot, A., Cole, D.K., Whale, A.D., Chillakuri, C.

(2022) Nat Commun 13: 5333

• DOI: https://doi.org/10.1038/s41467-022-32811-1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 95.42 kDa 
• Atom Count: 6,536 
• Modelled Residue Count: 811 
• Deposited Residue Count: 835 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A583ZB34 (Homo sapiens) Explore A0A583ZB34  Go to UniProtKB:  A0A583ZB34

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
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
KRAS G12D peptide (VVVGADGVGK)	C	10	Homo sapiens	Mutation(s): 1  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01111 (Homo sapiens) Explore P01111  Go to UniProtKB:  P01111
PHAROS:  P01111 GTEx:  ENSG00000213281

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR alpha	D	203	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR beta	E	246	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth E], G [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.156	α = 90
b = 144.156	β = 90
c = 119.592	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Karuppiah, V., Robinson, R.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description