6FML

CryoEM Structure INO80core Nucleosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.

Eustermann, S.Schall, K.Kostrewa, D.Lakomek, K.Strauss, M.Moldt, M.Hopfner, K.P.

(2018) Nature 556: 386-390

  • DOI: 10.1038/s41586-018-0029-y
  • Primary Citation of Related Structures:  
    6FHS, 6FML

  • PubMed Abstract: 
  • In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chro ...

    In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers 1-3 such as the 15-subunit INO80 complex 4 . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA 5-8 . The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA + ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data 8 suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange.


    Organizational Affiliation

    Center for Integrated Protein Science, Munich, Germany. hopfner@genzentrum.lmu.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like helicaseABC462Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0006820
EC: 3.6.4.12
Find proteins for G0RYI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like helicaseDEF488Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0006170
EC: 3.6.4.12
Find proteins for G0RYC2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ino80G1856Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
les2H491Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0004910
Find proteins for G0RY01 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ies6I219Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0032670
Find proteins for G0S590 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Actin related protein 5J770Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: CTHT_0032660
Find proteins for G0S589 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2MQ135Homo sapiensMutation(s): 0 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3DH3C15H3C14H3C13
Find proteins for Q71DI3 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  Q71DI3
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4NR102Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS  P62805
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1OS129Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS  P0C0S8
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IPT125Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62807 (Homo sapiens)
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PHAROS  P62807
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Nucleosomal DNA Strand 1K196synthetic construct
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Entity ID: 8
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Nucleosomal DNA Strand 2L196synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyEMBO ALTF 1098-2012
European Research CouncilGermanyATMMACHINE
German Research FoundationGermanyCRC1064, GRK1721

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other