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: RUVBL1, INO80H, NMP238, TIP49, TIP49A
EC: 3.6.4.12
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Find proteins for Q9Y265 (Homo sapiens)
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GTEx:  ENSG00000175792 
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UniProt GroupQ9Y265
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RuvB-like 2B, D, F463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2, INO80J, TIP48, TIP49B, CGI-46
EC: 3.6.4.12
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GTEx:  ENSG00000183207 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Chromatin-remodeling ATPase INO80G1290Homo sapiensMutation(s): 0 
Gene Names: INO80, INO80A, INOC1, KIAA1259
EC: 3.6.4
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GTEx:  ENSG00000128908 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Actin-related protein 5H607Homo sapiensMutation(s): 0 
Gene Names: ACTR5, ARP5
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GTEx:  ENSG00000101442 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1I, M136Homo sapiensMutation(s): 0 
Gene Names: 
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GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4J, N103Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EK, O130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA, H2AC4, H2AC8
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GTEx:  ENSG00000277075 ENSG00000278463 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JL, P126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR, H2BC11
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GTEx:  ENSG00000124635 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
INO80 complex subunit BQ [auth R]356Homo sapiensMutation(s): 0 
Gene Names: INO80B, HMGA1L4, PAPA1, ZNHIT4
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GTEx:  ENSG00000115274 
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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
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
T [auth A],
U [auth B],
V [auth C],
W [auth D],
X [auth E],
T [auth A],
U [auth B],
V [auth C],
W [auth D],
X [auth E],
Y [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
Z [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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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View more in-depth experimental data

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