Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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: 51.95 kDa 
• Atom Count: 3388 
• Modelled Residue Count: 383 
• Deposited Residue Count: 456 
• Unique protein chains: 3

1S7Q

Crystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants

• PDB DOI: 10.2210/pdb1S7Q/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-01-30 Released: 2004-05-04 
• Deposition Author(s): Velloso, L.M., Michaelsson, J., Ljunggren, H.G., Schneider, G., Achour, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition.

Velloso, L.M., Michaelsson, J., Ljunggren, H.G., Schneider, G., Achour, A.

(2004) J Immunol 172: 5504-5511

• PubMed: 15100292 
• DOI: 10.4049/jimmunol.172.9.5504
• Primary Citation of Related Structures:  
  1S7Q, 1S7R, 1S7S, 1S7T, 1S7U, 1S7V, 1S7W, 1S7X


• PubMed Abstract: 
  

Lymphocytic choriomeningitis virus infection of H-2(b) mice generates a strong CD8(+) CTL response mainly directed toward three immunodominant epitopes, one of which, gp33, is presented by both H-2D(b) and H-2K(b) MHC class I molecules. This CTL response acts as a selective agent for the emergence of viral escape variants. These variants generate altered peptide ligands (APLs) that, when presented by class I MHC molecules, antagonize CTL recognition and ultimately allow the virus to evade the cellular immune response. The emergence of APLs of the gp33 epitope is particularly advantageous for LCMV, as it allows viral escape in the context of both H-2D(b) and H-2K(b) MHC class I molecules. We have determined crystal structures of three different APLs of gp33 in complex with both H-2D(b) and H-2K(b). Comparison between these APL/MHC structures and those of the index gp33 peptide/MHC reveals the structural basis for three different strategies used by LCMV viral escape mutations: 1) conformational changes in peptide and MHC residues that are potential TCR contacts, 2) impairment of APL binding to the MHC peptide binding cleft, and 3) introduction of subtle changes at the TCR/pMHC interface, such as the removal of a single hydroxyl group.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A	348	Mus musculus	Mutation(s): 0  Gene Names: H2-K, H2-K1
UniProt
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: 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
Glycoprotein 9-residue peptide	C	9	N/A	Mutation(s): 0
UniProt
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE)) Explore P07399  Go to UniProtKB:  P07399

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.22	α = 90
b = 135.871	β = 90
c = 45.168	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-30 
• Released Date: 2004-05-04 
Deposition Author(s): Velloso, L.M., Michaelsson, J., Ljunggren, H.G., Schneider, G., Achour, A.

Revision History  

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection