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Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor

X-ray diffraction
2.21Å resolution
PDB entry 3d2u coloured by chain, front view.
PDB entry 3d2u coloured by chain, side view.
PDB entry 3d2u coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
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: 27564.69 Å2
Buried surface area: 8908.84 Å2
Dissociation area: 1,091.74 Å2
Dissociation energy (ΔGdiss): 0.49 kcal/mol
Dissociation entropy (TΔSdiss): 13.02 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-140175
Assembly 2
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Multimeric state: hetero tetramer
Accessible surface area: 27257.46 Å2
Buried surface area: 8005.87 Å2
Dissociation area: 1,098.11 Å2
Dissociation energy (ΔGdiss): 0.87 kcal/mol
Dissociation entropy (TΔSdiss): 13.02 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-140175

Macromolecules

Glycoprotein UL18
Chains: A, E
Length: 281 amino acids
Theoretical weight: 31.66 KDa
Source organism: Human betaherpesvirus 5
UniProt:
  • Canonical: P08560 (Residues: 21-301; Coverage: 80%)
Gene names: H301, UL18
Pfam:
InterPro:
CATH:
Glycoprotein UL18 in PDB entry 3d2u, assembly 1, front view.
Glycoprotein UL18 in PDB entry 3d2u, assembly 1, side view.
Glycoprotein UL18 in PDB entry 3d2u, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P08560  
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Beta-2-microglobulin
Chains: B, F
Length: 99 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Pfam: Immunoglobulin C1-set domain
InterPro:
CATH: Immunoglobulins
SCOP: C1 set domains (antibody constant domain-like)
Beta-2-microglobulin in PDB entry 3d2u, assembly 1, front view.
Beta-2-microglobulin in PDB entry 3d2u, assembly 1, side view.
Beta-2-microglobulin in PDB entry 3d2u, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P61769  
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Leukocyte immunoglobulin-like receptor subfamily B member 1
Chains: D, H
Length: 198 amino acids
Theoretical weight: 22.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q8NHL6 (Residues: 24-221; Coverage: 32%)
Gene names: ILT2, LILRB1, LIR1, MIR7
Pfam: Immunoglobulin domain
InterPro:
CATH: Immunoglobulins
SCOP: I set domains
Leukocyte immunoglobulin-like receptor subfamily B member 1 in PDB entry 3d2u, assembly 1, front view.
Leukocyte immunoglobulin-like receptor subfamily B member 1 in PDB entry 3d2u, assembly 1, side view.
Leukocyte immunoglobulin-like receptor subfamily B member 1 in PDB entry 3d2u, assembly 1, top view.
PDBe-KB: UniProt Coverage View: Q8NHL6  
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Actin, cytoplasmic 1, N-terminally processed
Chains: C, G
Length: 9 amino acids
Theoretical weight: 1.01 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P60709 (Residues: 170-178; Coverage: 2%)
Gene name: ACTB
Actin, cytoplasmic 1, N-terminally processed in PDB entry 3d2u, assembly 1, front view.
Actin, cytoplasmic 1, N-terminally processed in PDB entry 3d2u, assembly 1, side view.
Actin, cytoplasmic 1, N-terminally processed in PDB entry 3d2u, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P60709  
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