› 6mlc

X-ray diffraction
1.8Å resolution

PHD6 domain of MLL3 in complex with histone H4

Released:
DOI: 10.2210/pdb6mlc/pdb
PDB entry 6mlc coloured by chain, front view.
PDB entry 6mlc coloured by chain, side view.
PDB entry 6mlc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4.
Liu Y, Qin S, Chen TY, Lei M, Dhar SS, Ho JC, Dong A, Loppnau P, Li Y, Lee MG, Min J
Nat Commun 10 36 (2019)
PMID: 30604749

Function and Biology Details

Reaction catalysed: 
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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158699 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase 2C Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 92 amino acids
Theoretical weight: 10.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8NEZ4 (Residues: 1055-1144; Coverage: 2%)
Gene names: HALR, KIAA1506, KMT2C, MLL3
Histone H4 Chains: E, F
Molecule details ›
Chains: E, F
Length: 20 amino acids
Theoretical weight: 2 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 2-21; Coverage: 19%)
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

Ligands and Environments

3 bound ligands:
Ligand ZN 14 x ZN
Ligand GOL 5 x GOL
Ligand UNX 7 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P6
Unit cell:
a: 85.939Å b: 85.939Å c: 98.733Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.194 0.216
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

7 review citations

COMPASS and SWI/SNF complexes in development and disease.
Cenik et al. (2021)
6 more

1 mention without citation

Atypical histone targets of PHD fingers.
Black et al. (2023)