7S8F

STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PEPTIDE AND BOUND GLYCEROL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of phosphopeptide neoantigen immunogenicity.

Patskovsky, Y.Natarajan, A.Patskovska, L.Nyovanie, S.Joshi, B.Morin, B.Brittsan, C.Huber, O.Gordon, S.Michelet, X.Schmitzberger, F.Stein, R.B.Findeis, M.A.Hurwitz, A.Van Dijk, M.Chantzoura, E.Yague, A.S.Pollack Smith, D.Buell, J.S.Underwood, D.Krogsgaard, M.

(2023) Nat Commun 14: 3763-3763

  • DOI: https://doi.org/10.1038/s41467-023-39425-1
  • Primary Citation of Related Structures:  
    7RZD, 7RZJ, 7S79, 7S7D, 7S8A, 7S8E, 7S8F, 7S8I, 7S8J

  • PubMed Abstract: 

    Altered protein phosphorylation in cancer cells often leads to surface presentation of phosphopeptide neoantigens. However, their role in cancer immunogenicity remains unclear. Here we describe a mechanism by which an HLA-B*0702-specific acute myeloid leukemia phosphoneoantigen, pMLL 747-755 (EPR(pS)PSHSM), is recognized by a cognate T cell receptor named TCR27, a candidate for cancer immunotherapy. We show that the replacement of phosphoserine P 4 with serine or phosphomimetics does not affect pMHC conformation or peptide-MHC affinity but abrogates TCR27-dependent T cell activation and weakens binding between TCR27 and pMHC. Here we describe the crystal structures for TCR27 and cognate pMHC, map of the interface produced by nuclear magnetic resonance, and a ternary complex generated using information-driven protein docking. Our data show that non-covalent interactions between the epitope phosphate group and TCR27 are crucial for TCR specificity. This study supports development of new treatment options for cancer patients through target expansion and TCR optimization.


  • Organizational Affiliation

    Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-7 alpha chain275Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo 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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MLL cleavage product N320 peptide9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens)
Explore Q03164 
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
Entity Groups  
UniProt GroupQ03164
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.571α = 90
b = 65.571β = 90
c = 238.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM124489

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-18
    Changes: Refinement description