› 9dg3

Electron Microscopy
3.46Å resolution

ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome

Released:
DOI: 10.2210/pdb9dg3/pdb
PDB entry 9dg3 coloured by chain, front view.
PDB entry 9dg3 coloured by chain, side view.
PDB entry 9dg3 coloured by chain, top view.
Source organisms:
Primary publication:
Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1.
López VG, Valencia-Sánchez MI, Abini-Agbomson S, Thomas JF, Lee R, De Ioannes P, Sosa BA, Armache JP, Armache KJ
Nature 636 755-761 (2024)
PMID: 39537923
Related structures: EMD-46822

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-283125 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chain: C
Histone H2B 1.1 Chains: D, H
Histone H2A type 1 Chain: G
RING1 and YY1-binding protein Chain: M
Ubiquitin Chain: N
DNA (187-MER) Chain: I
DNA (187-MER) Chain: J

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.46Å
Relevant EMDB volumes: EMD-46822
Expression system: Escherichia coli

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