8AV6

CryoEM structure of INO80 core nucleosome complex in closed grappler conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanism of extranucleosomal DNA readout by the INO80 complex.

Kunert, F.Metzner, F.J.Jung, J.Hopfler, M.Woike, S.Schall, K.Kostrewa, D.Moldt, M.Chen, J.X.Bantele, S.Pfander, B.Eustermann, S.Hopfner, K.P.

(2022) Sci Adv 8: eadd3189-eadd3189

  • DOI: https://doi.org/10.1126/sciadv.add3189
  • Primary Citation of Related Structures:  
    8A5A, 8A5D, 8A5O, 8A5P, 8A5Q, 8ATF, 8AV6

  • PubMed Abstract: 

    The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.


  • Organizational Affiliation

    Institute of Molecular Biology (IMB), Mainz, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like helicase
A, B, C
462Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0006820
EC: 3.6.4.12
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Find proteins for G0RYI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like helicase
D, E, F
488Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0006170
EC: 3.6.4.12
UniProt
Find proteins for G0RYC2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ino801,856Thermochaetoides thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PAPA-1 domain-containing protein492Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0004910
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
YL1_C domain-containing protein219Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0032670
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DASH complex subunit DAD4769Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0032660
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
M, Q
135Homo sapiensMutation(s): 0 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3D
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
N, R
102Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
O, S
129Homo sapiensMutation(s): 0 
Gene Names: LOC112656772LOC112674385
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/I
P, T
125Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA227DNA molecule
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (208-MER)227DNA molecule
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union833613 INO3D
German Research Foundation (DFG)GermanyCRC1064
German Research Foundation (DFG)GermanyCRC1361
German Research Foundation (DFG)GermanyRTG1721
German Research Foundation (DFG)GermanyGottfried-Wilhelm-Leibniz Prize

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references