› 6bx3

Electron Microscopy
4.3Å resolution

Structure of histone H3k4 methyltransferase

Released:
DOI: 10.2210/pdb6bx3/pdb
PDB entry 6bx3 coloured by chain, front view.
PDB entry 6bx3 coloured by chain, side view.
PDB entry 6bx3 coloured by chain, top view.
Source organisms:
Primary publication:
Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex.
Qu Q, Takahashi YH, Yang Y, Hu H, Zhang Y, Brunzelle JS, Couture JF, Shilatifard A, Skiniotis G
Cell 174 1117-1126.e12 (2018)
PMID: 30100186
Related structures: EMD-7303

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
PDBe Complex ID:
PDB-CPX-108183 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Histone-lysine N-methyltransferase, H3 lysine-4 specific Chain: E
Molecule details ›
Chain: E
Length: 278 amino acids
Theoretical weight: 32.16 KDa
Source organism: Saccharomyces cerevisiae YJM789
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A6ZT27 (Residues: 799-1076; Coverage: 26%)
Gene names: SCY_2511, SET1
Sequence domains:
COMPASS component BRE2 Chain: K
Molecule details ›
Chain: K
Length: 417 amino acids
Theoretical weight: 48.31 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P43132 (Residues: 87-503; Coverage: 83%)
Gene names: BRE2, CPS60, YLR015W
COMPASS component SDC1 Chains: M, N
Molecule details ›
Chains: M, N
Length: 42 amino acids
Theoretical weight: 4.81 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q03323 (Residues: 122-163; Coverage: 24%)
Gene names: CPS25, SAF19, SDC1, YDR469W
Sequence domains: Dpy-30 motif
COMPASS component SPP1 Chain: F
Molecule details ›
Chain: F
Length: 237 amino acids
Theoretical weight: 28.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q03012 (Residues: 117-353; Coverage: 67%)
Gene names: CPS40, SAF41, SPP1, YPL138C
COMPASS component SWD1 Chain: B
Molecule details ›
Chain: B
Length: 412 amino acids
Theoretical weight: 47.05 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P39706 (Residues: 2-413; Coverage: 97%)
Gene names: CPS50, FUN16, SAF49, SWD1, YAR003W
Sequence domains: WD domain, G-beta repeat
COMPASS component SWD3 Chain: A
Molecule details ›
Chain: A
Length: 314 amino acids
Theoretical weight: 34.66 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P38123 (Residues: 2-315; Coverage: 100%)
Gene names: CPS30, SAF35, SWD3, YBR1237, YBR175W
Sequence domains: WD domain, G-beta repeat

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.3Å
Relevant EMDB volumes: EMD-7303
Expression system: Spodoptera frugiperda

Quick links

Citations

13 review citations

Epigenetic modifications of histones in cancer.
Zhao et al. (2019)
12 more

7 mentions without citation

Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast.
Separovich et al. (2021)
6 more