1VAC

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

PDB 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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901 Go to UniProtKB: P01901
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01901
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Reference Sequence

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(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01887
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Reference Sequence

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