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Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h bound at SHL-2

Electron Microscopy
3.9Å resolution
PDB entry 6ne3 coloured by chain, front view.
PDB entry 6ne3 coloured by chain, side view.
PDB entry 6ne3 coloured by chain, top view.
Source organisms:
Assembly composition:
hetero undecamer (preferred)
Entry contents: 6 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 94136.65 Å2
Buried surface area: 63657.28 Å2
Dissociation area: 6,223.58 Å2
Dissociation energy (ΔGdiss): 75.99 kcal/mol
Dissociation entropy (TΔSdiss): 16.38 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-120333

Macromolecules

Histone H3.2
Chains: A, E
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 6ne3, assembly 1, front view.
Histone H3.2 in PDB entry 6ne3, assembly 1, side view.
Histone H3.2 in PDB entry 6ne3, assembly 1, top view.
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Histone H4
Chains: B, F
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 6ne3, assembly 1, front view.
Histone H4 in PDB entry 6ne3, assembly 1, side view.
Histone H4 in PDB entry 6ne3, assembly 1, top view.
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Histone H2A type 1
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.09 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Pfam:
InterPro:
Histone H2A type 1 in PDB entry 6ne3, assembly 1, front view.
Histone H2A type 1 in PDB entry 6ne3, assembly 1, side view.
Histone H2A type 1 in PDB entry 6ne3, assembly 1, top view.
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Histone H2B 1.1
Chain: D
Length: 99 amino acids
Theoretical weight: 11.18 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 28-126; Coverage: 79%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, front view.
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, side view.
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, top view.
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Histone H2B 1.1
Chain: H
Length: 93 amino acids
Theoretical weight: 10.35 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 33-125; Coverage: 74%)
Pfam: Core histone H2A/H2B/H3/H4
InterPro:
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, front view.
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, side view.
Histone H2B 1.1 in PDB entry 6ne3, assembly 1, top view.
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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5
Chain: W
Length: 467 amino acids
Theoretical weight: 54.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O60264 (Residues: 166-634; Coverage: 44%)
Gene names: SMARCA5, SNF2H, WCRF135
Pfam:
InterPro:
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 in PDB entry 6ne3, assembly 1, front view.
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 in PDB entry 6ne3, assembly 1, side view.
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 in PDB entry 6ne3, assembly 1, top view.
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DNA chain J
Name: DNA (156-MER)
Representative chains: J
Length: 156 nucleotides
Theoretical weight: 47.94 KDa
DNA (156-MER) in PDB entry 6ne3, assembly 1, front view.
DNA (156-MER) in PDB entry 6ne3, assembly 1, side view.
DNA (156-MER) in PDB entry 6ne3, assembly 1, top view.
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DNA chain I
Name: DNA (156-MER)
Representative chains: I
Length: 156 nucleotides
Theoretical weight: 48.37 KDa
DNA (156-MER) in PDB entry 6ne3, assembly 1, front view.
DNA (156-MER) in PDB entry 6ne3, assembly 1, side view.
DNA (156-MER) in PDB entry 6ne3, assembly 1, top view.
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