4NNX | pdb_00004nnx

Crystal structure of PKD2 phosphopeptide bound to HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.

Mohammed, F.Stones, D.H.Zarling, A.L.Willcox, C.R.Shabanowitz, J.Cummings, K.L.Hunt, D.F.Cobbold, M.Engelhard, V.H.Willcox, B.E.

(2017) Oncotarget 8: 54160-54172

  • DOI: https://doi.org/10.18632/oncotarget.16952
  • Primary Citation Related Structures: 
    4NNX, 4NNY, 4NO0, 4NO2, 4NO3, 4NO5

  • PubMed Abstract: 

    Dysregulated post-translational modification provides a source of altered self-antigens that can stimulate immune responses in autoimmunity, inflammation, and cancer. In recent years, phosphorylated peptides have emerged as a group of tumour-associated antigens presented by MHC molecules and recognised by T cells, and represent promising candidates for cancer immunotherapy. However, the impact of phosphorylation on the antigenic identity of phosphopeptide epitopes is unclear. Here we examined this by determining structures of MHC-bound phosphopeptides bearing canonical position 4-phosphorylations in the presence and absence of their phosphate moiety, and examining phosphopeptide recognition by the T cell receptor (TCR). Strikingly, two peptides exhibited major conformational changes upon phosphorylation, involving a similar molecular mechanism, which focussed changes on the central peptide region most critical for T cell recognition. In contrast, a third epitope displayed little conformational alteration upon phosphorylation. In addition, binding studies demonstrated TCR interaction with an MHC-bound phosphopeptide was both epitope-specific and absolutely dependent upon phosphorylation status. These results highlight the critical influence of phosphorylation on the antigenic identity of naturally processed class I MHC epitopes. In doing so they provide a molecular framework for understanding phosphopeptide-specific immune responses, and have implications for the development of phosphopeptide antigen-specific cancer immunotherapy approaches.


  • Organizational Affiliation
    • Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.

Macromolecule Content 

  • Total Structure Weight: 45.06 kDa 
  • Atom Count: 3,353 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 382 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain274Homo sapiensMutation(s): 0 
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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo 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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase D29Homo sapiensMutation(s): 0 
EC: 2.7.11.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZL6 (Homo sapiens)
Explore Q9BZL6 
Go to UniProtKB:  Q9BZL6
PHAROS:  Q9BZL6
GTEx:  ENSG00000105287 
Entity Groups
UniProt GroupQ9BZL6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.1α = 90
b = 79.8β = 90
c = 111.3γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary