› 8t9f

Electron Microscopy
2.6Å resolution

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1

Released:
DOI: 10.2210/pdb8t9f/pdb
PDB entry 8t9f coloured by chain, front view.
PDB entry 8t9f coloured by chain, side view.
PDB entry 8t9f coloured by chain, top view.
Source organisms:
Primary publication:
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell 83 2872-2883.e7 (2023)
PMID: 37595555
Related structures: EMD-41109

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-240152 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone-lysine N-methyltransferase KMT5B Chain: K
Molecule details ›
Chain: K
Length: 393 amino acids
Theoretical weight: 44.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q4FZB7 (Residues: 1-392; Coverage: 44%)
  • Best match: Q4FZB7-2 (Residues: 1-393)
Gene names: CGI-85, KMT5B, SUV420H1
Sequence domains: SET domain
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.4 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2A.Z Chains: C, G
Molecule details ›
Chains: C, G
Length: 128 amino acids
Theoretical weight: 13.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P0C0S5 (Residues: 1-128; Coverage: 100%)
Gene names: H2AFZ, H2AZ, H2AZ1
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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
DNA (122-MER) Chain: I
Molecule details ›
Chain: I
Length: 146 nucleotides
Theoretical weight: 44.82 KDa
DNA (122-MER) Chain: J
Molecule details ›
Chain: J
Length: 146 nucleotides
Theoretical weight: 45.3 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.6Å
Relevant EMDB volumes: EMD-41109
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

1 review citation

Regulation of the heterochromatin spreading reaction by trans-acting factors.
Hamali et al. (2023)