› 5f6k

X-ray diffraction
2.41Å resolution

Crystal structure of the MLL3-Ash2L-RbBP5 complex

Released:
DOI: 10.2210/pdb5f6k/pdb
PDB entry 5f6k coloured by chain, front view.
PDB entry 5f6k coloured by chain, side view.
PDB entry 5f6k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for activity regulation of MLL family methyltransferases.
Li Y, Han J, Zhang Y, Cao F, Liu Z, Li S, Wu J, Hu C, Wang Y, Shuai J, Chen J, Cao L, Li D, Shi P, Tian C, Zhang J, Dou Y, Li G, Chen Y, Lei M
Nature 530 447-52 (2016)
PMID: 26886794

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero heptamer
hetero trimer
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-172250 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Set1/Ash2 histone methyltransferase complex subunit ASH2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 184 amino acids
Theoretical weight: 20.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBL3 (Residues: 380-496, 516-598; Coverage: 28%)
Gene names: ASH2L, ASH2L1
Sequence domains: SPRY domain
Structure domains: Jelly Rolls
Histone-lysine N-methyltransferase 2C Chains: C, E
Molecule details ›
Chains: C, E
Length: 159 amino acids
Theoretical weight: 18.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NEZ4 (Residues: 4757-4911; Coverage: 3%)
Gene names: HALR, KIAA1506, KMT2C, MLL3
Sequence domains: SET domain
Structure domains: SET domain
Retinoblastoma-binding protein 5 Chains: D, F
Molecule details ›
Chains: D, F
Length: 27 amino acids
Theoretical weight: 3.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15291 (Residues: 330-356; Coverage: 5%)
Gene names: RBBP5, RBQ3
Histone H3.3C Chain: M
Molecule details ›
Chain: M
Length: 9 amino acids
Theoretical weight: 1.06 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q6NXT2 (Residues: 2-10; Coverage: 7%)
Gene names: H3-5, H3F3C

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand SAH 2 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21212
Unit cell:
a: 80.342Å b: 236.076Å c: 44.416Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.18 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

33 review citations

Writing, erasing and reading histone lysine methylations.
Hyun et al. (2017)
32 more

11 mentions without citation

Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases.
Worden et al. (2019)
10 more