4NNX

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 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.18632/oncotarget.16952
  • Primary Citation of Related Structures:  
    4NO0, 4NO2, 4NO3, 4NO5, 4NNX, 4NNY

  • 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-associat ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chainA274Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-2-microglobulinB99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
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PHAROS  P61769
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase D2C9Homo sapiensMutation(s): 0 
Gene Names: PRKD2PKD2HSPC187
EC: 2.7.11.13
Find proteins for Q9BZL6 (Homo sapiens)
Explore Q9BZL6 
Go to UniProtKB:  Q9BZL6
NIH Common Fund Data Resources
PHAROS  Q9BZL6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
CL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • 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 

  • 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