› 8v27

Electron Microscopy
3.34Å resolution

H2BK120ub-modified nucleosome ubiquitin position 3

Released:
DOI: 10.2210/pdb8v27/pdb
PDB entry 8v27 coloured by chain, front view.
PDB entry 8v27 coloured by chain, side view.
PDB entry 8v27 coloured by chain, top view.
Source organisms:
Primary publication:
Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.
Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Wolberger C
Nucleic Acids Res (2024)
PMID: 39149911
Related structures: EMD-42900

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-513343 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 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 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 123 amino acids
Theoretical weight: 13.63 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Ubiquitin Chain: K
Molecule details ›
Chain: K
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
601 DNA (147-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
601 DNA (147-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.34Å
Relevant EMDB volumes: EMD-42900
Expression system: Escherichia coli

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