1CE6

MHC CLASS I H-2DB COMPLEXED WITH A SENDAI VIRUS NUCLEOPROTEIN PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of two H-2Db/glycopeptide complexes suggest a molecular basis for CTL cross-reactivity.

Glithero, A.Tormo, J.Haurum, J.S.Arsequell, G.Valencia, G.Edwards, J.Springer, S.Townsend, A.Pao, Y.L.Wormald, M.Dwek, R.A.Jones, E.Y.Elliott, T.

(1999) Immunity 10: 63-74

  • DOI: 10.1016/s1074-7613(00)80007-2
  • Primary Citation of Related Structures:  
    1CE6, 1QLF

  • PubMed Abstract: 
  • Two synthetic O-GlcNAc-bearing peptides that elicit H-2Db-restricted glycopeptide-specific cytotoxic T cells (CTL) have been shown to display nonreciprocal patterns of cross-reactivity. Here, we present the crystal structures of the H-2Db glycopeptide complexes to 2 ...

    Two synthetic O-GlcNAc-bearing peptides that elicit H-2Db-restricted glycopeptide-specific cytotoxic T cells (CTL) have been shown to display nonreciprocal patterns of cross-reactivity. Here, we present the crystal structures of the H-2Db glycopeptide complexes to 2.85 A resolution or better. In both cases, the glycan is solvent exposed and available for direct recognition by the T cell receptor (TCR). We have modeled the complex formed between the MHC-glycopeptide complexes and their respective TCRs, showing that a single saccharide residue can be accommodated in the standard TCR-MHC geometry. The models also reveal a possible molecular basis for the observed cross-reactivity patterns of the CTL clones, which appear to be influenced by the length of the CDR3 loop and the nature of the immunizing ligand.


    Organizational Affiliation

    Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (MHC CLASS I H-2DB HEAVY CHAIN)A274Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
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Go to UniProtKB:  P01899
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UniProt GroupP01899
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HUMAN BETA-2 MICROGLOBULIN)B108Homo 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
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SENDAI VIRUS NUCLEOPROTEIN)C9N/AMutation(s): 0 
UniProt
Find proteins for P04858 (Sendai virus (strain Z))
Explore P04858 
Go to UniProtKB:  P04858
Entity Groups  
UniProt GroupP04858
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.787α = 90
b = 58.082β = 108.26
c = 74.666γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-07
    Changes: Database references