6JQ3

Crystal Structure of H2-Kb in complex with a DPAGT1 mutant peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy.

Bai, P.Li, Y.Zhou, Q.Xia, J.Wei, P.C.Deng, H.Wu, M.Chan, S.K.Kappler, J.W.Zhou, Y.Tran, E.Marrack, P.Yin, L.

(2021) Oncoimmunology 10: 1868130-1868130

  • DOI: 10.1080/2162402X.2020.1868130
  • Primary Citation of Related Structures:  
    6JQ2, 6JQ3, 6JTP, 6JTN

  • PubMed Abstract: 
  • Genetic mutations lead to the production of mutated proteins from which peptides are presented to T cells as cancer neoantigens. Evidence suggests that T cells that target neoantigens are the main mediators of effective cancer immunotherapies. Although algorithms have been used to predict neoantigens, only a minority are immunogenic ...

    Genetic mutations lead to the production of mutated proteins from which peptides are presented to T cells as cancer neoantigens. Evidence suggests that T cells that target neoantigens are the main mediators of effective cancer immunotherapies. Although algorithms have been used to predict neoantigens, only a minority are immunogenic. The factors that influence neoantigen immunogenicity are not completely understood. Here, we classified human neoantigen/neopeptide data into three categories based on their TCR-pMHC binding events. We observed a conservative mutant orientation of the anchor residue from immunogenic neoantigens which we termed the "NP" rule. By integrating this rule with an existing prediction algorithm, we found improved performance in neoantigen prioritization. To better understand this rule, we solved several neoantigen/MHC structures. These structures showed that neoantigens that follow this rule not only increase peptide-MHC binding affinity but also create new TCR-binding features. These molecular insights highlight the value of immune-based classification in neoantigen studies and may enable the design of more effective cancer immunotherapies.


    Organizational Affiliation

    State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chainA274Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
UniProt
Find proteins for P01901 (Mus musculus)
Explore P01901 
Go to UniProtKB:  P01901
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DPAGT1 mutant antigen SIIVFNLLB [auth P]8Mus musculusMutation(s): 0 
EC: 2.7.8.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3H5 (Homo sapiens)
Explore Q9H3H5 
Go to UniProtKB:  Q9H3H5
PHAROS:  Q9H3H5
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinC [auth B]99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.63α = 90
b = 67.97β = 103.86
c = 70.73γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2021-02-17
    Changes: Database references