7OW3 | pdb_00007ow3

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

PDB DOI: https://doi.org/10.2210/pdb7OW3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.260 (Depositor), 0.269 (DCC)
R-Value Work:
0.228 (Depositor), 0.236 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OW3

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 178.31 kDa
Atom Count: 12,705
Modeled Residue Count: 1,530
Deposited Residue Count: 1,540
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D, G, J	275	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A0A583ZB34 (Homo sapiens) Explore A0A583ZB34 Go to UniProtKB: A0A583ZB34
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A583ZB34
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
KRAS peptide (VVVGAGGVGK)	C, F, I, L	10	Homo sapiens	Mutation(s): 0 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01111
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.260 (Depositor), 0.269 (DCC)
R-Value Work: 0.228 (Depositor), 0.236 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.854	α = 90
b = 117.028	β = 99.3
c = 110.643	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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
Version 1.3: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.