8wg5

Electron Microscopy
3.05Å resolution

Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome

Released:

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).
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-270964 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Ubiquitin carboxyl-terminal hydrolase 16 Chain: M
Molecule details ›
Chain: M
Length: 823 amino acids
Theoretical weight: 93.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5T5 (Residues: 1-823; Coverage: 100%)
Gene names: MSTP039, USP16
Sequence domains:
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 98 amino acids
Theoretical weight: 11.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 38-135; Coverage: 72%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Histone H2A type 1-B/E Chains: C, G
Histone H2B type 1-K Chains: D, H
Ubiquitin Chain: U
DNA (147-MER) Chain: I
DNA (147-MER) Chain: J

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.05Å
Relevant EMDB volumes: EMD-37503
Expression system: Escherichia coli