› 6fml

Electron Microscopy
4.34Å resolution

CryoEM Structure INO80core Nucleosome complex

Released:
DOI: 10.2210/pdb6fml/pdb
PDB entry 6fml coloured by chain, front view.
PDB entry 6fml coloured by chain, side view.
PDB entry 6fml coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.
Eustermann S, Schall K, Kostrewa D, Lakomek K, Strauss M, Moldt M, Hopfner KP
Nature 556 386-390 (2018)
PMID: 29643509
Related structures: EMD-4277

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-119912 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 distinct):
RuvB-like helicase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 462 amino acids
Theoretical weight: 50.45 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
UniProt:
  • Canonical: G0RYI5 (Residues: 1-462; Coverage: 100%)
Gene name: CTHT_0006820
Sequence domains:
RuvB-like helicase Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 488 amino acids
Theoretical weight: 53.21 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
UniProt:
  • Canonical: G0RYC2 (Residues: 1-488; Coverage: 100%)
Gene name: CTHT_0006170
Sequence domains:
Ino80 Chain: G
Molecule details ›
Chain: G
Length: 1856 amino acids
Theoretical weight: 210.44 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
INO80 complex subunit B-like conserved region domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 491 amino acids
Theoretical weight: 52.02 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
UniProt:
  • Canonical: G0RY01 (Residues: 1-492; Coverage: 100%)
Gene name: CTHT_0004910
Sequence domains: PAPA-1-like conserved region
Vps72/YL1 C-terminal domain-containing protein Chain: I
Molecule details ›
Chain: I
Length: 219 amino acids
Theoretical weight: 23.13 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
UniProt:
  • Canonical: G0S590 (Residues: 1-219; Coverage: 100%)
Gene name: CTHT_0032670
Sequence domains: YL1 nuclear protein C-terminal domain
Actin related protein 5 Chain: J
Molecule details ›
Chain: J
Length: 770 amino acids
Theoretical weight: 86 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Trichoplusia ni
UniProt:
  • Canonical: G0S589 (Residues: 98-616, 617-866; Coverage: 89%)
Gene name: CTHT_0032660
Sequence domains: Actin
Histone H3.2 Chains: M, Q
Molecule details ›
Chains: M, Q
Length: 135 amino acids
Theoretical weight: 15.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q71DI3 (Residues: 2-136; Coverage: 99%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: N, R
Molecule details ›
Chains: N, R
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 2-103; Coverage: 99%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: O, S
Molecule details ›
Chains: O, S
Length: 129 amino acids
Theoretical weight: 13.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C0S8 (Residues: 2-130; Coverage: 99%)
Gene names: H2AC11, H2AC13, H2AC15, H2AC16, H2AC17, H2AFC, H2AFD, H2AFI, H2AFN, H2AFP, HIST1H2AG, HIST1H2AI, HIST1H2AK, HIST1H2AL, HIST1H2AM
Sequence domains:
Histone H2B type 1-C/E/F/G/I Chains: P, T
Molecule details ›
Chains: P, T
Length: 125 amino acids
Theoretical weight: 13.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62807 (Residues: 2-126; Coverage: 99%)
Gene names: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI
Sequence domains: Core histone H2A/H2B/H3/H4
Nucleosomal DNA Strand 1 Chain: K
Molecule details ›
Chain: K
Length: 196 nucleotides
Theoretical weight: 60.65 KDa
Nucleosomal DNA Strand 2 Chain: L
Molecule details ›
Chain: L
Length: 196 nucleotides
Theoretical weight: 60.38 KDa

Ligands and Environments

2 bound ligands:
Ligand ADP 6 x ADP
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.34Å
Relevant EMDB volumes: EMD-4277
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

22 review citations

Chromatin Remodelers in the 3D Nuclear Compartment.
Magaña-Acosta et al. (2020)
21 more

14 mentions without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
13 more