PDBe 6ppb

Electron Microscopy
4.3Å resolution

Kaposi's sarcoma-associated herpesvirus (KSHV), C5 portal vertex structure

Released:
Related structures: EMD-20432

Function and Biology Details

Reaction catalysed:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Capsid vertex component 1 Chain: k
Molecule details ›
Chain: k
Length: 454 amino acids
Theoretical weight: 49.59 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q76RH8 (Residues: 1-454; Coverage: 100%)
Gene names: CVC1, ORF32
Sequence domains: Herpesvirus UL17 protein
Capsid vertex component 2 Chains: l, m
Molecule details ›
Chains: l, m
Length: 549 amino acids
Theoretical weight: 61.49 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q76RI7 (Residues: 1-549; Coverage: 100%)
Gene names: CVC2, ORF19
Sequence domains: Herpesvirus UL25 family
Large tegument protein deneddylase Chains: n, o
Molecule details ›
Chains: n, o
Length: 2635 amino acids
Theoretical weight: 290.02 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q2HR64 (Residues: 1-2635; Coverage: 100%)
Gene name: ORF64
Sequence domains: Herpesvirus tegument protein, N-terminal conserved region
Major capsid protein Chains: S, T, W, X
Molecule details ›
Chains: S, T, W, X
Length: 1376 amino acids
Theoretical weight: 153.57 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q2HRA7 (Residues: 1-1376; Coverage: 100%)
Gene names: MCP, ORF25
Sequence domains: Herpes virus major capsid protein
Triplex capsid protein 1 Chains: 5, b
Molecule details ›
Chains: 5, b
Length: 331 amino acids
Theoretical weight: 36.37 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q76RF6 (Residues: 1-331; Coverage: 100%)
Gene names: ORF62, TRX1
Sequence domains: Herpesvirus capsid shell protein VP19C
Triplex capsid protein 2 Chains: 6, 7, c, d
Molecule details ›
Chains: 6, 7, c, d
Length: 305 amino acids
Theoretical weight: 34.28 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q98832 (Residues: 1-305; Coverage: 100%)
Gene name: TRX2
Sequence domains: Herpesvirus VP23 like capsid protein
Small capsomere-interacting protein Chains: 0, 1, 2, 3
Molecule details ›
Chains: 0, 1, 2, 3
Length: 170 amino acids
Theoretical weight: 18.6 KDa
Source organism: Human herpesvirus 8 strain GK18
UniProt:
  • Canonical: Q76RF4 (Residues: 1-170; Coverage: 100%)
Gene names: ORF65, SCP
Sequence domains: Gammaherpesvirus capsid protein

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.3Å
Relevant EMDB volumes: EMD-20432