Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 45513.95 
• Atom Count: 3196 
• Residue Count: 381 
• Unique protein chains: 3

1KBG

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

• DOI: 10.2210/pdb1KBG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vesicular stomatitis Indiana virus (strain Glasgow), Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): 1 


• Deposited: 1998-08-28 Released: 1999-02-09 
• Deposition Author(s): Speir, J.A., Abdel-Motal, U.M., Jondal, M., Wilson, I.A.

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Experimental Data Snapshot

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

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: 10023770 


• 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. 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)	H	274	Mus musculus	Mutation(s): 0  Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus) Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (BETA-2-MICROGLOBULIN)	L	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Go to UniProtKB:  P01887

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)	P	8	Vesicular stomatitis Indiana virus (strain Glasgow)	Mutation(s): 1  Gene Names: N
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow)) Go to UniProtKB:  P11212

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FUC	H	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
GAL	P	BETA-D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
NAG	H	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLA	P	ALPHA D-GALACTOSE C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ESC	P	L-PEPTIDE LINKING	C6 H13 N O2 S		MET

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 = 135.870	α = 90.00
b = 86.840	β = 90.00
c = 44.980	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
SCALEPACK	data scaling
X-PLOR	model building
DENZO	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-28 
• Released Date: 1999-02-09 
• Deposition Author(s): Speir, J.A., Abdel-Motal, U.M., Jondal, M., Wilson, I.A.

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