6X00

Structure of DbNA(11) peptides bound to H-2Db MHC-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Overlapping Peptides Elicit Distinct CD8 + T Cell Responses following Influenza A Virus Infection.

Assmus, L.M.Guan, J.Wu, T.Farenc, C.Sng, X.Y.X.Zareie, P.Nguyen, A.Nguyen, A.T.Tscharke, D.C.Thomas, P.G.Rossjohn, J.Gras, S.Croft, N.P.Purcell, A.W.La Gruta, N.L.

(2020) J Immunol 205: 1731-1742

  • DOI: https://doi.org/10.4049/jimmunol.2000689
  • Primary Citation of Related Structures:  
    6WZY, 6X00

  • PubMed Abstract: 

    The presentation of pathogen-derived peptides on MHC class I molecules is essential for the initiation of adaptive CD8 + T cell immunity, which in turn is critical for effective control of many significant human infections. The identification of immunogenic pathogen-derived epitopes and a detailed understanding of how they are recognized by TCRs is essential for the design of effective T cell-based vaccines. In this study, we have characterized the T cell recognition and immune responses in mice to two naturally presented influenza A virus-derived peptides previously identified from virally infected cells via mass spectrometry. These neuraminidase-derived peptides, NA 181-190 (SGPDNGAVAV) and NA 181-191 (SGPDNGAVAVL), are completely overlapping with the exception of a 1 aa extension at the C terminus of the longer peptide. This minor peptidic difference results in the induction of two completely independent and non-cross-reactive T cell populations that show distinct functional characteristics after influenza A virus infection of B6 mice. We show that the unique TCR reactivity to the overlapping peptides is present in the naive repertoire prior to immune expansion in B6 mice. Moreover, we provide a structural explanation underlying the distinct CD8 + T cell reactivities, which reinforces the concept that peptide length is a key determinant of Ag specificity in CD8 + T cell responses.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain281Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
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UniProt GroupP01899
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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 
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Epitope from Neuraminidase Protein (NA-181-191)11Influenza A virusMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for P03468 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03468 
Go to UniProtKB:  P03468
Entity Groups  
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UniProt GroupP03468
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.01α = 90
b = 44.751β = 98.45
c = 71.657γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description