1KBG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 2.1 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

  • DOI: 10.1016/s1074-7613(00)80006-0
  • Primary Citation of Related Structures:  
    1KBG

  • 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 that express both alpha/beta TCR, specific for glycopeptide, and gamma/delta TCR, specific for the disaccharide, even on glycolipids ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)A [auth H]274Mus musculusMutation(s): 0 
Gene Names: H2-K1H2-K
UniProt
Find proteins for P01901 (Mus musculus)
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Go to UniProtKB:  P01901
Entity Groups  
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UniProt GroupP01901
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BETA-2-MICROGLOBULIN)B [auth L]99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)C [auth P]8N/AMutation(s): 1 
UniProt
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow))
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Go to UniProtKB:  P11212
Entity Groups  
UniProt GroupP11212
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranoseE [auth B]2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G67988RO
GlyCosmos:  G67988RO
GlyGen:  G67988RO
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth H]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ESC
Query on ESC
C [auth P]L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.87α = 90
b = 86.84β = 90
c = 44.98γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary