› 5hq2

X-ray diffraction
4.5Å resolution

Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle

Released:
DOI: 10.2210/pdb5hq2/pdb
PDB entry 5hq2 coloured by chain, front view.
PDB entry 5hq2 coloured by chain, side view.
PDB entry 5hq2 coloured by chain, top view.
Source organisms:
Primary publication:
Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.
Girish TS, McGinty RK, Tan S
J Mol Biol 428 1531-43 (2016)
PMID: 26953260

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 hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-118751 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.2 Chain: A
Molecule details ›
Chain: A
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chain: G
Molecule details ›
Chain: G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
Length: 122 amino acids
Theoretical weight: 13.52 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Guanine nucleotide exchange factor SRM1 Chain: K
Molecule details ›
Chain: K
Length: 483 amino acids
Theoretical weight: 53.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21827 (Residues: 2-482; Coverage: 100%)
Gene names: MTR1, PRP20, SRM1, YGL097W
Sequence domains:
N-lysine methyltransferase KMT5A Chain: M
Molecule details ›
Chain: M
Length: 202 amino acids
Theoretical weight: 23.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NQR1 (Residues: 194-393; Coverage: 51%)
Gene names: KMT5A, PRSET7, SET07, SET8, SETD8
Sequence domains: SET domain
DNA (149-MER) Chain: I
Molecule details ›
Chain: I
Length: 149 nucleotides
Theoretical weight: 45.77 KDa
DNA (149-MER) Chain: J
Molecule details ›
Chain: J
Length: 149 nucleotides
Theoretical weight: 46.21 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2221
Unit cell:
a: 100.729Å b: 300.752Å c: 182.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.342 0.339 0.397
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

The emerging role of lysine methyltransferase SETD8 in human diseases.
Milite et al. (2016)
6 more

3 mentions without citation

Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.
Girish et al. (2016)
2 more