2VAA

MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 919-927

  • DOI: https://doi.org/10.1126/science.1323877
  • Primary Citation of Related Structures:  
    2VAA, 2VAB

  • PubMed Abstract: 

    The x-ray structures of a murine MHC class I molecule (H-2Kb) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein (52-59), VSV-8, and the Sendai virus nucleoprotein (324-332), SEV-9. The H-2Kb complexes were refined at 2.3 A for VSV-8 and 2.5 A for SEV-9. The structure of H-2Kb exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the H-2Kb binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by the insertion of a bulge in the center of an otherwise beta conformation. Most of the specific interactions are between side-chain atoms of H-2Kb and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in H-2Kb are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC CLASS I H-2KB HEAVY CHAIN274Mus musculusMutation(s): 0 
Gene Names: BETA-2-MICROGLOBULIN
UniProt
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-2 MICROGLOBULIN99Mus musculusMutation(s): 0 
Gene Names: BETA-2-MICROGLOBULIN
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VESICULAR STOMATITIS VIRUS NUCLEOPROTEINC [auth P]8Vesicular stomatitis virusMutation(s): 0 
UniProt
Find proteins for P11212 (Vesicular stomatitis Indiana virus (strain Glasgow))
Go to UniProtKB:  P11212
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.1α = 90
b = 88.9β = 90
c = 45.7γ = 90
Software Package:
Software NamePurpose
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-06-20
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-06-05
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-10-23
    Changes: Structure summary