Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFERI


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MHC-Binding
Epitope  
   
Complex PDB ID 3FOL
Accession Number 3DIEP0571
IEDB ID 135864
Epitope Sequence VNDIFERI
Starting Position1
Ending Position8
Epitope Type Linear Epitope

Assay Information  
Assay Antigen Purified MHC - X-ray crystallography Structure (crystal; NMR; etc.)
PDB CategoryIMMUNE SYSTEM
Keyword Class I MHC; peptide complex; Diabetes-protective Effect; Immune response; Immunoglobulin domain; MHC I; Polymorphism; Secreted; Acetylation; Chromosomal protein; DNA-binding; Methylation; Nucleosome core; Nucleus; Phosphoprotein; Ubl conjugation; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain A
Antigen PDB ChainP
CommentsH-2Kb and H-2Kd; the allele naturally present in NOD mice; share 90 and 85% sequence identity with H-2Kwm7; respectively (Fig. 2A and B). Structural comparison of H-2Kb [PDB: 1KPU] and H-2Kd [PDB: 1VGK] with H-2Kwm7 in this complex with VNDIFERI peptide shows that the quaternary structure of H-2Kwm7 conforms to the canonical MHC fold (Fig. 3A). Crystallographic analysis did not provide an explanation for the remarkable conservation of Arg at P7 of the peptides purified from H-2Kwm7 molecules (Table 1; Fig. 1D); as this residue was found to be solvent exposed rather than serving as an anchor.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.5
R-Value
0.196
Space Group
C 1 2 1
Unit Cell
Length(Å) Angle(°)
a = 117.393 α = 90
b = 66.63 β = 93.66
c = 56.211 γ = 90



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Source Information  
Structure Determination Method X-RAY DIFFRACTION