6HTS

Cryo-EM structure of the human INO80 complex bound to nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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

Structure and regulation of the human INO80-nucleosome complex.

Ayala, R.Willhoft, O.Aramayo, R.J.Wilkinson, M.McCormack, E.A.Ocloo, L.Wigley, D.B.Zhang, X.

(2018) Nature 556: 391-395

  • DOI: 10.1038/s41586-018-0021-6
  • Primary Citation of Related Structures:  
    6HTS

  • PubMed Abstract: 
  • Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines 1 ...

    Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines 1 . Biochemical studies 2-4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes 5-7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding 8 , histone exchange 9 and nucleosome spacing 10-12 remain poorly understood. Although some remodellers work as monomers 13 , others work as highly cooperative dimers 11, 14, 15 . Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.


    Organizational Affiliation

    Section of Structural Biology, Dept. Medicine, Imperial College London, London, UK. xiaodong.zhang@imperial.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like 1A, C, E456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1INO80HNMP238TIP49TIP49A
EC: 3.6.4.12
Find proteins for Q9Y265 (Homo sapiens)
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PHAROS:  Q9Y265
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like 2B, D, F463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2INO80JTIP48TIP49BCGI-46
EC: 3.6.4.12
Find proteins for Q9Y230 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin-remodeling ATPase INO80G1290Homo sapiensMutation(s): 0 
Gene Names: INO80INO80AINOC1KIAA1259
EC: 3.6.4
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PHAROS:  Q9ULG1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 5H607Homo sapiensMutation(s): 0 
Gene Names: ACTR5ARP5
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PHAROS:  Q9H9F9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1I, M136Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4J, N103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EK, O130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JL, P126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
INO80 complex subunit BQ [auth R]356Homo sapiensMutation(s): 0 
Gene Names: INO80BHMGA1L4PAPA1ZNHIT4
Find proteins for Q9C086 (Homo sapiens)
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Entity ID: 10
MoleculeChainsLengthOrganismImage
DNA (150-MER)R [auth X]228synthetic construct
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Entity ID: 11
MoleculeChainsLengthOrganismImage
DNA (150-MER)S [auth Y]228synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098412/Z/12/Z
Wellcome TrustUnited Kingdom095519/Z/11/Z
Cancer Research UKUnited KingdomC6913/A21608

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Other