› 6pwv

Electron Microscopy
6.2Å resolution

Cryo-EM structure of MLL1 core complex bound to the nucleosome

Released:
DOI: 10.2210/pdb6pwv/pdb
PDB entry 6pwv coloured by chain, front view.
PDB entry 6pwv coloured by chain, side view.
PDB entry 6pwv 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-20512

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 hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-120470 (preferred)
Entry contents:
9 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (11 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: 122 amino acids
Theoretical weight: 13.52 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
Protein dpy-30 homolog Chains: E, F
Molecule details ›
Chains: E, F
Length: 102 amino acids
Theoretical weight: 11.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9C005 (Residues: 1-99; Coverage: 100%)
Gene name: DPY30
Sequence domains: Dpy-30 motif
Set1/Ash2 histone methyltransferase complex subunit ASH2 Chain: D
Molecule details ›
Chain: D
Length: 534 amino acids
Theoretical weight: 60.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBL3 (Residues: 96-628; Coverage: 85%)
Gene names: ASH2L, ASH2L1
Sequence domains:
DNA (147-MER) Chain: O
Molecule details ›
Chain: O
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (147-MER) Chain: P
Molecule details ›
Chain: P
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 6.2Å
Relevant EMDB volumes: EMD-20512
Expression system: Escherichia coli

Quick links

Citations

8 review citations

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

6 mentions without citation

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