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: 44.30 kDa 
• Atom Count: 3238 
• Residue Count: 382 
• Unique protein chains: 3

2VAB

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

• DOI: 10.2210/pdb2VAB/pdb
• Entry: 2VAB supersedes: 1VAB

• Classification: COMPLEX (MHC I/PEPTIDE)
• Organism(s): Mus musculus, Murine respirovirus
• 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: 0.159 
• R-Value Observed: 0.159 

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

• PubMed: 1323877 
• DOI: 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.

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Related Citations: 

• 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

• 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.

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
SENDAI VIRUS NUCLEOPROTEIN	P	9	Murine respirovirus	Mutation(s): 0
Find proteins for P04857 (Sendai virus (strain Enders)) Explore P04857  Go to UniProtKB:  P04857

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139	α = 90
b = 90.4	β = 90
c = 46.3	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.
• This entry supersedes: 1VAB

Revision History 

• 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