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› 6ypt

X-ray diffraction
3.66Å resolution

X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin

Released:
DOI: 10.2210/pdb6ypt/pdb
Model geometry
Fit model/data
PDB entry 6ypt coloured by chain, front view.
PDB entry 6ypt coloured by chain, side view.
PDB entry 6ypt coloured by chain, top view.
Source organisms:
Primary publication:
X-ray structure of Turnip Yellow Mosaic Virus PRO/DUB in complex with Ubiquitin
Fieulaine S, Bressanelli S
J. Biol. Chem. (2020)

Function and Biology Details

Reactions catalysed: 
RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate.
Thiol-dependent hydrolysis of ester, thioester, amide, peptide andisopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residueprotein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143337 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Methyltransferase/Protease/Ubiquitinyl hydrolase Chains: A, C
Molecule details ›
Chains: A, C
Length: 160 amino acids
Theoretical weight: 17.78 KDa
Source organism: Turnip yellow mosaic virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P10358 (Residues: 728-879; Coverage: 8%)
Sequence domains: Tymovirus endopeptidase
Ubiquitin Chains: B, D
Molecule details ›
Chains: B, D
Length: 85 amino acids
Theoretical weight: 9.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 599-599, 609-683; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand GVE 2 x GVE
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 37.93Å b: 51.86Å c: 125.25Å
α: 90° β: 98.37° γ: 90°
R-values:
R R work R free
0.209 0.206 0.283
Expression system: Escherichia coli

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