7OW4

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

• PDB DOI: https://doi.org/10.2210/pdb7OW4/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): Coles, C.H., Karuppiah, V., Robinson, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.249 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

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 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 179.41 kDa 
• Atom Count: 13,589 
• Modelled Residue Count: 1,532 
• Deposited Residue Count: 1,544 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D, G, J	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, E, H, K	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, F, I, L	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	M [auth D], N [auth G], O [auth H], P [auth J], Q [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.249 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.224	α = 90
b = 121.432	β = 90
c = 127.863	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

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