› 6pww

Electron Microscopy
4.4Å resolution

Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome

Released:
DOI: 10.2210/pdb6pww/pdb
PDB entry 6pww coloured by chain, front view.
PDB entry 6pww coloured by chain, side view.
PDB entry 6pww coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US
Nat Commun 10 5540 (2019)
PMID: 31804488
Related structures: EMD-20513

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 tridecamer (preferred)
PDBe Complex ID:
PDB-CPX-120471 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
Retinoblastoma-binding protein 5 Chain: A
Molecule details ›
Chain: A
Length: 538 amino acids
Theoretical weight: 59.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15291 (Residues: 2-538; Coverage: 100%)
Gene names: RBBP5, RBQ3
Sequence domains: WD domain, G-beta repeat
WD repeat-containing protein 5 Chain: B
Molecule details ›
Chain: B
Length: 313 amino acids
Theoretical weight: 34.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61964 (Residues: 22-334; Coverage: 94%)
Gene names: BIG3, WDR5
Sequence domains: WD domain, G-beta repeat
MLL cleavage product C180 Chain: C
Molecule details ›
Chain: C
Length: 209 amino acids
Theoretical weight: 24.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q03164 (Residues: 3762-3969; Coverage: 5%)
Gene names: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, MLL1, TRX1
Sequence domains: SET domain
Histone H3.2 Chains: G, K
Molecule details ›
Chains: G, K
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: H, L
Molecule details ›
Chains: H, L
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: I, M
Molecule details ›
Chains: I, M
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: J, N
Molecule details ›
Chains: J, N
Length: 123 amino acids
Theoretical weight: 13.66 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
DNA (146-MER) Chain: O
Molecule details ›
Chain: O
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (146-MER) Chain: P
Molecule details ›
Chain: P
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

2 bound ligands:
Ligand SAH 1 x SAH
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-20513
Expression system: Escherichia coli

Quick links

Citations

10 review citations

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

2 mentions without citation

The engagement of histone lysine methyltransferases with nucleosomes: structural basis, regulatory mechanisms, and therapeutic implications.
Li et al. (2023)
1 more