Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 45.46 kDa 
• Atom Count: 3304 
• Modelled Residue Count: 381 
• Deposited Residue Count: 381 
• Unique protein chains: 3

1KBG

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

• PDB DOI: 10.2210/pdb1KBG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• 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: 2.20 Å
• R-Value Free: 0.279 
• R-Value Work: 0.224 
• R-Value Observed: 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 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)	A [auth H]	274	Mus musculus	Mutation(s): 0  Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BETA-2-MICROGLOBULIN)	B [auth L]	99	Mus musculus	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)	C [auth P]	8	N/A	Mutation(s): 1
UniProt
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow)) Explore P11212  Go to UniProtKB:  P11212

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose	E [auth B]	2		N/A
Glycosylation Resources
GlyTouCan:  G67988RO GlyCosmos:  G67988RO GlyGen:  G67988RO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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

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 = 135.87	α = 90
b = 86.84	β = 90
c = 44.98	γ = 90

Software Package:

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

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
  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