› 6px3

Electron Microscopy
4.1Å resolution

Set2 bound to nucleosome

Released:
DOI: 10.2210/pdb6px3/pdb
PDB entry 6px3 coloured by chain, front view.
PDB entry 6px3 coloured by chain, side view.
PDB entry 6px3 coloured by chain, top view.
Source organisms:
Primary publication:
Nucleosome and ubiquitin position Set2 to methylate H3K36.
Bilokapic S, Halic M
Nat Commun 10 3795 (2019)
PMID: 31439846
Related structures: EMD-20517

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-120474 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.3C 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: P02302 (Residues: 1-136; Coverage: 100%)
Gene names: h3-5, h3f3c
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; Ubiquitin Chains: C, G
Molecule details ›
Chains: C, G
Length: 221 amino acids
Theoretical weight: 24.05 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P0CH09 (Residues: 1-75; Coverage: 59%)
  • Canonical: P06897 (Residues: 18-130; Coverage: 87%)
Gene names: RPL40B, UBI2, YKR094C
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 123 amino acids
Theoretical weight: 13.66 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
Histone-lysine N-methyltransferase, H3 lysine-36 specific Chain: S
Molecule details ›
Chain: S
Length: 939 amino acids
Theoretical weight: 105.43 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Escherichia coli
UniProt:
  • Canonical: G0S676 (Residues: 1-939; Coverage: 100%)
Gene name: CTHT_0025760
Sequence domains:
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 149 nucleotides
Theoretical weight: 45.76 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 149 nucleotides
Theoretical weight: 46.22 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-20517
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
8 more

3 mentions without citation

Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications.
Vaughan et al. (2021)
2 more