› 6kix

Electron Microscopy
4.1Å resolution

Cryo-EM structure of human MLL1-NCP complex, binding mode1

Released:
DOI: 10.2210/pdb6kix/pdb
PDB entry 6kix coloured by chain, front view.
PDB entry 6kix coloured by chain, side view.
PDB entry 6kix coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J
Nature 573 445-449 (2019)
PMID: 31485071
Related structures: EMD-0694

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-120157 (preferred)
Entry contents:
8 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (10 distinct):
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
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.5 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Retinoblastoma-binding protein 5 Chain: N
Molecule details ›
Chain: N
Length: 538 amino acids
Theoretical weight: 59.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15291 (Residues: 1-538; Coverage: 100%)
Gene names: RBBP5, RBQ3
Sequence domains: WD domain, G-beta repeat
MLL cleavage product C180 Chain: K
Molecule details ›
Chain: K
Length: 216 amino acids
Theoretical weight: 24.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03164 (Residues: 3754-3969; Coverage: 5%)
Gene names: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, MLL1, TRX1
Sequence domains: SET domain
WD repeat-containing protein 5 Chain: R
Molecule details ›
Chain: R
Length: 334 amino acids
Theoretical weight: 36.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61964 (Residues: 1-334; Coverage: 100%)
Gene names: BIG3, WDR5
Sequence domains: WD domain, G-beta repeat
Set1/Ash2 histone methyltransferase complex subunit ASH2 Chain: T
Molecule details ›
Chain: T
Length: 534 amino acids
Theoretical weight: 60.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBL3 (Residues: 95-628; Coverage: 85%)
Gene names: ASH2L, ASH2L1
Sequence domains:
DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

4 bound ligands:
Ligand SAH 1 x SAH
Ligand ZN 1 x ZN
Ligand LYS 1 x LYS
Ligand GLN 1 x GLN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-0694
Expression system: Escherichia coli

Quick links

Citations

20 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
19 more

5 mentions without citation

Insights on the regulation of the MLL/SET1 family histone methyltransferases.
Sha et al. (2020)
4 more