› 7d1z

Electron Microscopy
3.15Å resolution

Cryo-EM structure of SET8-nucleosome complex

Released:
DOI: 10.2210/pdb7d1z/pdb
PDB entry 7d1z coloured by chain, front view.
PDB entry 7d1z coloured by chain, side view.
PDB entry 7d1z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase.
Ho CH, Takizawa Y, Kobayashi W, Arimura Y, Kimura H, Kurumizaka H
Life Sci Alliance 4 (2021)
PMID: 33574035
Related structures: EMD-30551

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H4]-L-lysine(20) = S-adenosyl-L-homocysteine + a [histone H4]-N(6)-methyl-L-lysine(20)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121187 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 139 amino acids
Theoretical weight: 15.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P68431 (Residues: 2-136; Coverage: 99%)
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
Molecule details ›
Chains: B, F
Length: 106 amino acids
Theoretical weight: 11.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1-B/E Chains: C, G
Molecule details ›
Chains: C, G
Length: 133 amino acids
Theoretical weight: 14.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04908 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC4, H2AC8, H2AFA, H2AFM, HIST1H2AB, HIST1H2AE
Sequence domains:
Histone H2B type 1-J Chains: D, H
Molecule details ›
Chains: D, H
Length: 129 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 2-126; Coverage: 99%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
N-lysine methyltransferase KMT5A Chain: K
Molecule details ›
Chain: K
Length: 352 amino acids
Theoretical weight: 39.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NQR1 (Residues: 45-62, 63-393; Coverage: 89%)
Gene names: KMT5A, PRSET7, SET07, SET8, SETD8
Sequence domains: SET domain
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.15Å
Relevant EMDB volumes: EMD-30551
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Is There a Histone Code for Cellular Quiescence?
Bonitto et al. (2021)
1 more

4 mentions without citation

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