6O53

Structure of HLA-A2:01 with peptide MM96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Anin silico-in vitroPipeline Identifying an HLA-A*02:01+KRAS G12V+Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients.

Mishto, M.Mansurkhodzhaev, A.Ying, G.Bitra, A.Cordfunke, R.A.Henze, S.Paul, D.Sidney, J.Urlaub, H.Neefjes, J.Sette, A.Zajonc, D.M.Liepe, J.

(2019) Front Immunol 10: 2572-2572

  • DOI: 10.3389/fimmu.2019.02572
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting CD8 <sup>+ </sup> T cells to recurrent tumor-specific mutations can profoundly contribute to cancer treatment. Some of these mutations are potential tumor antigens although they can be displayed by non-spliced epitopes only in a few patient ...

    Targeting CD8 + T cells to recurrent tumor-specific mutations can profoundly contribute to cancer treatment. Some of these mutations are potential tumor antigens although they can be displayed by non-spliced epitopes only in a few patients, because of the low affinity of the mutated non-spliced peptides for the predominant HLA class I alleles. Here, we describe a pipeline that uses the large sequence variety of proteasome-generated spliced peptides and identifies spliced epitope candidates, which carry the mutations and bind the predominant HLA-I alleles with high affinity. They could be used in adoptive T cell therapy and other anti-cancer immunotherapies for large cohorts of cancer patients. As a proof of principle, the application of this pipeline led to the identification of a KRAS G12V mutation-carrying spliced epitope candidate, which is produced by proteasomes, transported by TAPs and efficiently presented by the most prevalent HLA class I molecules, HLA-A * 02:01 complexes.


    Organizational Affiliation

    Division of Immune Regulation, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Institut für Biochemie, Berlin, Germany.,Department of Medicine, University of California, San Diego, San Diego, CA, United States.,Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Quantitative and Systems Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Institut for Clinical Chemistry, University Medical Center Goettingen Bioanalytics, Goettingen, Germany.,Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center LUMC, Leiden, Netherlands.,Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom.,Department of Immunohematology and Bloodbank, Leiden University Medical Center LUMC, Leiden, Netherlands.,Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A
Find proteins for U5YJM1 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  U5YJM1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MM96
C
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.247α = 90.00
b = 79.638β = 116.12
c = 57.227γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release