RCSB PDB - 8K50: Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK)

 8K50

Crystal structure of HLA-A*11:01 in complex with KRAS G12V peptide (VVVGARGVGK)

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

  • Deposited: 2023-07-20 Released: 2025-01-29 
  • Deposition Author(s): Xu, K.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of HLA-A*11:01 in complex with KRAS G12R peptide (VVVGARGVGK)

Xu, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A alpha chain
A, D, G, J
276Homo sapiensMutation(s): 3 
Gene Names: HLA-AHLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E, H, K
122Homo 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
KRAS G12V peptide (VVVGAVGVGK)
C, F, I, L
10Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.289α = 90
b = 121.845β = 90
c = 133.376γ = 90
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
Cootmodel building
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-29 
  • Deposition Author(s): Xu, K.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA1302200

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release