Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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: 56.08 kDa 
• Atom Count: 3210 
• Modelled Residue Count: 383 
• Deposited Residue Count: 494 
• Unique protein chains: 3

1BII

THE CRYSTAL STRUCTURE OF H-2DD MHC CLASS I IN COMPLEX WITH THE HIV-1 DERIVED PEPTIDE P18-110

• PDB DOI: 10.2210/pdb1BII/pdb

• Classification: COMPLEX (MHC I/PEPTIDE)
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-11 Released: 1998-10-14 
• Deposition Author(s): Achour, A., Persson, K., Harris, R.A., Sundback, J., Sentman, C.L., Lindqvist, Y., Schneider, G., Karre, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.323 
• R-Value Work: 0.278 

Literature

The crystal structure of H-2Dd MHC class I complexed with the HIV-1-derived peptide P18-I10 at 2.4 A resolution: implications for T cell and NK cell recognition.

Achour, A., Persson, K., Harris, R.A., Sundback, J., Sentman, C.L., Lindqvist, Y., Schneider, G., Karre, K.

(1998) Immunity 9: 199-208

• PubMed: 9729040 
• DOI: 10.1016/s1074-7613(00)80602-0
• Primary Citation of Related Structures:  
  1BII


• PubMed Abstract: 
  

The structure of H-2Dd complexed with the HIV-derived peptide P18-I10 (RGPGRAFVTI) has been determined by X-ray crystallography at 2.4 A resolution. This MHC class I molecule has an unusual binding motif with four anchor residues in the peptide (G2, P3, R/K/H5, and I/L/F9 or 10). The cleft architecture of H-2Dd includes a deep narrow passage accomodating the N-terminal part of the peptide, explaining the obligatory G2P3 anchor motif. Toward the C-terminal half of the peptide, p5R to p8V form a type I' reverse turn; residues p6A to p9T, and in particular p7F, are readily exposed. The structure is discussed in relation to functional data available for T cell and natural killer cell recognition of the H-2Dd molecule.

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Related Citations: 

• Murine Mhc Class I H-2Dd Complex: Expression, Refolding and Crystallisation
  Achour, A., Harris, R.A., Persson, K., Sundback, J., Sentman, C.L., Schneider, G., Lindqvist, Y., Karre, K.
  () To be published --: --

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Organizational Affiliation: 

Microbiology and Tumor Biology Center, Karolinska Hospital, Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS I H-2DD	A	365	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01900 (Mus musculus) Explore P01900  Go to UniProtKB:  P01900

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-2 MICROGLOBULIN	B	119	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
DECAMERIC PEPTIDE	C [auth P]	10	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.323 
• R-Value Work: 0.278 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.26	α = 90
b = 92.53	β = 90
c = 108.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-11 
• Released Date: 1998-10-14 
Deposition Author(s): Achour, A., Persson, K., Harris, R.A., Sundback, J., Sentman, C.L., Lindqvist, Y., Schneider, G., Karre, K.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance