1QLF

MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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This is version 1.4 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., Elliot, T.

(1999) Immunity 10: 63

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

  • 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 glycopeptid ...

    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
MHC CLASS I H-2DB HEAVY CHAINA276Mus 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
HUMAN BETA-2-MICROGLOBULINB99Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
GTEx  ENSG00000166710
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SYNTHETIC GLYCOPEPTIDEC9Murine respirovirusMutation(s): 1 
Find proteins for P04857 (Sendai virus (strain Enders))
Explore P04857 
Go to UniProtKB:  P04857
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.073α = 90
b = 58.272β = 108.57
c = 77.146γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1999-08-30 
  • Released Date: 1999-09-01 
    • Deposition Author(s): Tormo, J., Jones, E.Y.

Revision History 

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary