6WZY

Structure of DbNA(10) peptides bound to H-2Db MHC-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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This is version 1.1 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: 10.4049/jimmunol.2000689
  • Primary Citation of Related Structures:  
    6X00, 6WZY

  • 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 identifica ...

    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; nathan.croft@monash.edu anthony.purcell@monash.edu nicole.la.gruta@monash.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chainA279Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
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
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Epitope from Neuraminidase Protein (NA-181-190)C10Influenza A virusMutation(s): 0 
EC: 3.2.1.18
Find proteins for P03468 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03468 
Go to UniProtKB:  P03468
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.722α = 90
b = 44.969β = 98.23
c = 71.774γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references