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Recognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C

X-ray diffraction
3.3Å resolution
PDB entry 5j6g coloured by chain, front view.
PDB entry 5j6g coloured by chain, side view.
PDB entry 5j6g coloured by chain, top view.
Source organism: Mus musculus
Assemblies composition:
hetero tetramer (preferred)
hetero octamer
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetramer
Accessible surface area: 22491.95 Å2
Buried surface area: 6355.83 Å2
Dissociation area: 1,172.41 Å2
Dissociation energy (ΔGdiss): -1.34 kcal/mol
Dissociation entropy (TΔSdiss): 12.23 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134982
Assembly 2
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Multimeric state: hetero tetramer
Accessible surface area: 22924.73 Å2
Buried surface area: 6396.75 Å2
Dissociation area: 1,164.69 Å2
Dissociation energy (ΔGdiss): -1.98 kcal/mol
Dissociation entropy (TΔSdiss): 12.24 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-134982
Assembly 3
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Multimeric state: hetero octamer
Accessible surface area: 43926.56 Å2
Buried surface area: 14242.7 Å2
Dissociation area: 2,337.1 Å2
Dissociation energy (ΔGdiss): -6.01 kcal/mol
Dissociation entropy (TΔSdiss): 27.16 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135112

Macromolecules

H-2 class I histocompatibility antigen, Q10 alpha chain
Chains: A, C
Length: 300 amino acids
Theoretical weight: 34.59 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01898 (Residues: 25-280; Coverage: 85%)
Gene name: H2-Q10
Pfam:
InterPro:
CATH:
H-2 class I histocompatibility antigen, Q10 alpha chain in PDB entry 5j6g, assembly 1, front view.
H-2 class I histocompatibility antigen, Q10 alpha chain in PDB entry 5j6g, assembly 1, side view.
H-2 class I histocompatibility antigen, Q10 alpha chain in PDB entry 5j6g, assembly 1, top view.
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Beta-2-microglobulin
Chains: B, D
Length: 100 amino acids
Theoretical weight: 11.79 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
Beta-2-microglobulin in PDB entry 5j6g, assembly 1, front view.
Beta-2-microglobulin in PDB entry 5j6g, assembly 1, side view.
Beta-2-microglobulin in PDB entry 5j6g, assembly 1, top view.
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Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
Chains: E, F
Length: 8 amino acids
Theoretical weight: 830 Da
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: Q9DBG6 (Residues: 373-380; Coverage: 1%)
Gene name: Rpn2
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 5j6g, assembly 1, front view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 5j6g, assembly 1, side view.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2 in PDB entry 5j6g, assembly 1, top view.
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Killer cell lectin-like receptor 3
Chains: G, H
Length: 132 amino acids
Theoretical weight: 15.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q64329 (Residues: 136-266; Coverage: 49%)
Gene names: Klra3, Ly-49c, Ly49C
Pfam: Lectin C-type domain
InterPro:
CATH: Mannose-Binding Protein A, subunit A
Killer cell lectin-like receptor 3 in PDB entry 5j6g, assembly 1, front view.
Killer cell lectin-like receptor 3 in PDB entry 5j6g, assembly 1, side view.
Killer cell lectin-like receptor 3 in PDB entry 5j6g, assembly 1, top view.
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