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Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide

X-ray diffraction
2.65Å resolution
PDB entry 2ve6 coloured by chain, front view.
PDB entry 2ve6 coloured by chain, side view.
PDB entry 2ve6 coloured by chain, top view.
Source organism: Mus musculus
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1
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Multimeric state: hetero trimer
Accessible surface area: 19602.99 Å2
Buried surface area: 4316.32 Å2
Dissociation area: 1,244.14 Å2
Dissociation energy (ΔGdiss): 3.78 kcal/mol
Dissociation entropy (TΔSdiss): 12.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135000
Assembly 2
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Multimeric state: hetero trimer
Accessible surface area: 18894.95 Å2
Buried surface area: 4443.78 Å2
Dissociation area: 1,307.69 Å2
Dissociation energy (ΔGdiss): 4.82 kcal/mol
Dissociation entropy (TΔSdiss): 12.06 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135000
Assembly 3
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Multimeric state: hetero trimer
Accessible surface area: 19777.53 Å2
Buried surface area: 4397.53 Å2
Dissociation area: 889.06 Å2
Dissociation energy (ΔGdiss): 6.22 kcal/mol
Dissociation entropy (TΔSdiss): 7.54 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135000
Assembly 4 (preferred)
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Multimeric state: hetero trimer
Accessible surface area: 19844.44 Å2
Buried surface area: 4297.25 Å2
Dissociation area: 1,239.29 Å2
Dissociation energy (ΔGdiss): 2.5 kcal/mol
Dissociation entropy (TΔSdiss): 12.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-135000

Macromolecules

H-2 class I histocompatibility antigen, D-B alpha chain
Chains: A, D, G, J
Length: 277 amino acids
Theoretical weight: 32.18 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01899 (Residues: 25-301; Coverage: 82%)
Gene name: H2-D1
Pfam:
InterPro:
CATH:
SCOP:
H-2 class I histocompatibility antigen, D-B alpha chain in PDB entry 2ve6, assembly 4, front view.
H-2 class I histocompatibility antigen, D-B alpha chain in PDB entry 2ve6, assembly 4, side view.
H-2 class I histocompatibility antigen, D-B alpha chain in PDB entry 2ve6, assembly 4, top view.
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Beta-2-microglobulin
Chains: B, E, H, K
Length: 99 amino acids
Theoretical weight: 11.68 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 2ve6, assembly 4, front view.
Beta-2-microglobulin in PDB entry 2ve6, assembly 4, side view.
Beta-2-microglobulin in PDB entry 2ve6, assembly 4, top view.
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SENDAI VIRUS EPITOPE RESIDUES 324-332 MODIFIED AT P7
Chains: C, F, I, L
Length: 9 amino acids
Theoretical weight: 1.04 KDa
SENDAI VIRUS EPITOPE RESIDUES 324-332 MODIFIED AT P7 in PDB entry 2ve6, assembly 4, front view.
SENDAI VIRUS EPITOPE RESIDUES 324-332 MODIFIED AT P7 in PDB entry 2ve6, assembly 4, side view.
SENDAI VIRUS EPITOPE RESIDUES 324-332 MODIFIED AT P7 in PDB entry 2ve6, assembly 4, top view.
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