Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 44.32 kDa 
• Atom Count: 3230 
• Residue Count: 381 
• Unique protein chains: 3

1VAC

MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND CHICKEN OVALBUMIN

• DOI: 10.2210/pdb1VAC/pdb

• Classification: COMPLEX (MHC I/PEPTIDE)
• Organism(s): Mus musculus, Gallus gallus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 1994-11-01 Released: 1996-06-20 
• Deposition Author(s): Fremont, D.H., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

Literature

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.

Fremont, D.H., Stura, E.A., Matsumura, M., Peterson, P.A., Wilson, I.A.

(1995) Proc Natl Acad Sci U S A 92: 2479-2483

• PubMed: 7708669 
• DOI: 10.1073/pnas.92.7.2479
• Primary Citation of Related Structures:  
  1VAC, 1VAD


• PubMed Abstract: 
  

Sequence analysis of peptides naturally presented by major histocompatibility complex (MHC) class I molecules has revealed allele-specific motifs in which the peptide length and the residues observed at certain positions are restricted. Nevertheless, peptides containing the standard motif often fail to bind with high affinity or form physiologically stable complexes. Here we present the crystal structure of a well-characterized antigenic peptide from ovalbumin [OVA-8, ovalbumin-(257-264), SIINFEKL] in complex with the murine MHC class I H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and Phe-P5 are packed closely together into binding pockets B and C, suggesting that the interplay of peptide anchor (P5) and secondary anchor (P2) residues can couple the preferred sequences at these positions. Comparison with the crystal structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9 (FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that the conserved water molecule that binds into the B pocket and mediates hydrogen bonding from the buried anchor hydroxyl group could not be likewise positioned if the P2 side chain were of significant size. Based on this structural evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering of these secondary submotifs from both crystallographic and immunological studies of MHC peptide binding should increase the accuracy of T-cell epitope prediction.

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Related Citations: 

• Crystal Structures of Two Viral Peptides in Complex with Murine Mhc Class I H-2Kb
  Fremont, D.H., Matsumura, M., Stura, E.A., Peterson, P.A., Wilson, I.A.
  (1992) Science 257: 919

• Emerging Principles for the Recognition of Peptide Antigens by Mhc Class I Molecules
  Matsumura, M., Fremont, D.H., Peterson, P.A., Wilson, I.A.
  (1992) Science 257: 927

• Crystallization of Murine Major Histocompatibility Complex Class I H-2Kb with Single Peptides
  Stura, E.A., Matsumura, M., Fremont, D.H., Saito, Y., Peterson, P.A., Wilson, I.A.
  (1992) J Mol Biol 228: 975

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS I H-2KB HEAVY CHAIN	A	274	Mus musculus	Mutation(s): 0  Gene Names: BETA-2-MICROGLOBULIN, H2-K1, H2-K
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2 MICROGLOBULIN	B	99	Mus musculus	Mutation(s): 0  Gene Names: BETA-2-MICROGLOBULIN, B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CHICKEN OVALBUMIN	P	8	Gallus gallus	Mutation(s): 0  Gene Names: SERPINB14
Find proteins for P01012 (Gallus gallus) Explore P01012  Go to UniProtKB:  P01012

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118	α = 90
b = 60.9	β = 107.6
c = 83.8	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-11-01 
• Released Date: 1996-06-20 
Deposition Author(s): Fremont, D.H., Wilson, I.A.

Revision History 

• Version 1.0: 1996-06-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance