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

Electron Microscopy
6.2Å resolution
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:
Assembly composition:
hetero hexadecamer (preferred)
Entry contents: 9 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexadecamer
Accessible surface area: 125978.86 Å2
Buried surface area: 66643.04 Å2
Dissociation area: 2,724.48 Å2
Dissociation energy (ΔGdiss): -20.11 kcal/mol
Dissociation entropy (TΔSdiss): 57.18 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120470

Macromolecules

Retinoblastoma-binding protein 5
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
Pfam: WD domain, G-beta repeat
InterPro:
Retinoblastoma-binding protein 5 in PDB entry 6pwv, assembly 1, front view.
Retinoblastoma-binding protein 5 in PDB entry 6pwv, assembly 1, side view.
Retinoblastoma-binding protein 5 in PDB entry 6pwv, assembly 1, top view.
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WD repeat-containing protein 5
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
Pfam: WD domain, G-beta repeat
InterPro:
WD repeat-containing protein 5 in PDB entry 6pwv, assembly 1, front view.
WD repeat-containing protein 5 in PDB entry 6pwv, assembly 1, side view.
WD repeat-containing protein 5 in PDB entry 6pwv, assembly 1, top view.
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MLL cleavage product C180
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
Pfam: SET domain
InterPro:
MLL cleavage product C180 in PDB entry 6pwv, assembly 1, front view.
MLL cleavage product C180 in PDB entry 6pwv, assembly 1, side view.
MLL cleavage product C180 in PDB entry 6pwv, assembly 1, top view.
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Histone H3.2
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%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H3.2 in PDB entry 6pwv, assembly 1, front view.
Histone H3.2 in PDB entry 6pwv, assembly 1, side view.
Histone H3.2 in PDB entry 6pwv, assembly 1, top view.
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Histone H4
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%)
Pfam: Centromere kinetochore component CENP-T histone fold
InterPro:
Histone H4 in PDB entry 6pwv, assembly 1, front view.
Histone H4 in PDB entry 6pwv, assembly 1, side view.
Histone H4 in PDB entry 6pwv, assembly 1, top view.
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Histone H2A type 1
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%)
Pfam:
InterPro:
Histone H2A type 1 in PDB entry 6pwv, assembly 1, front view.
Histone H2A type 1 in PDB entry 6pwv, assembly 1, side view.
Histone H2A type 1 in PDB entry 6pwv, assembly 1, top view.
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Histone H2B 1.1
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%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B 1.1 in PDB entry 6pwv, assembly 1, front view.
Histone H2B 1.1 in PDB entry 6pwv, assembly 1, side view.
Histone H2B 1.1 in PDB entry 6pwv, assembly 1, top view.
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Protein dpy-30 homolog
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
Pfam: Dpy-30 motif
InterPro:
Protein dpy-30 homolog in PDB entry 6pwv, assembly 1, front view.
Protein dpy-30 homolog in PDB entry 6pwv, assembly 1, side view.
Protein dpy-30 homolog in PDB entry 6pwv, assembly 1, top view.
Molecule details ›

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Set1/Ash2 histone methyltransferase complex subunit ASH2
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
Pfam:
InterPro:
Set1/Ash2 histone methyltransferase complex subunit ASH2 in PDB entry 6pwv, assembly 1, front view.
Set1/Ash2 histone methyltransferase complex subunit ASH2 in PDB entry 6pwv, assembly 1, side view.
Set1/Ash2 histone methyltransferase complex subunit ASH2 in PDB entry 6pwv, assembly 1, top view.
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DNA chain O
Name: DNA (147-MER)
Representative chains: O
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (147-MER) in PDB entry 6pwv, assembly 1, front view.
DNA (147-MER) in PDB entry 6pwv, assembly 1, side view.
DNA (147-MER) in PDB entry 6pwv, assembly 1, top view.
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DNA chain P
Name: DNA (147-MER)
Representative chains: P
Length: 147 nucleotides
Theoretical weight: 45.61 KDa
DNA (147-MER) in PDB entry 6pwv, assembly 1, front view.
DNA (147-MER) in PDB entry 6pwv, assembly 1, side view.
DNA (147-MER) in PDB entry 6pwv, assembly 1, top view.
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