1KBG

MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL.

Speir, J.A.Abdel-Motal, U.M.Jondal, M.Wilson, I.A.

(1999) Immunity 10: 51-61


  • PubMed Abstract: 
  • T cell receptor (TCR) recognition of nonpeptidic and modified peptide antigens has been recently uncovered but is still poorly understood. Immunization with an H-2Kb-restricted glycopeptide RGY8-6H-Gal2 generates a population of cytotoxic T cells tha ...

    T cell receptor (TCR) recognition of nonpeptidic and modified peptide antigens has been recently uncovered but is still poorly understood. Immunization with an H-2Kb-restricted glycopeptide RGY8-6H-Gal2 generates a population of cytotoxic T cells that express both alpha/beta TCR, specific for glycopeptide, and gamma/delta TCR, specific for the disaccharide, even on glycolipids. The crystal structure of Kb/RGY8-6H-Gal2 now demonstrates that the peptide and H-2Kb structures are unaffected by the peptide glycosylation, but the central region of the putative TCR binding site is dominated by the extensive exposure of the tethered carbohydrate. These features of the Kb/RGY8-6H-Gal2 structure are consistent with the individual ligand binding preferences identified for the alpha/beta and gamma/delta TCRs and thus explain the generation of a carbohydrate-specific T cell response.


    Related Citations: 
    • Immunization with Glycosylated Kb-Binding Peptides Generates Carbohydrate- Specific, Unrestricted Cytotoxic T Cells
      Abdel-Motal, U.M.,Berg, L.,Rosen, A.,Bengtsson, M.,Thorpe, C.J.,Kihlberg, J.,Dahmen, J.,Magnusson, G.,Karlsson, K.,Jondal, M.
      (1996) Eur.J.Immunol. 26: 544


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)
H
274Mus musculusGene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BETA-2-MICROGLOBULIN)
L
99Mus musculusGene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)
P
8Vesicular stomatitis Indiana virus (strain Glasgow)Gene Names: N
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow))
Go to UniProtKB:  P11212
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
H
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
P
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
P
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ESC
Query on ESC
P
L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.870α = 90.00
b = 86.840β = 90.00
c = 44.980γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance