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: https://doi.org/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 . 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. d.wigley@imperial.ac.uk.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 1
A, C, E
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1INO80HNMP238TIP49TIP49A
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y265 (Homo sapiens)
Explore Q9Y265 
Go to UniProtKB:  Q9Y265
GTEx:  ENSG00000175792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y265
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like 2
B, D, F
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2INO80JTIP48TIP49BCGI-46
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y230 (Homo sapiens)
Explore Q9Y230 
Go to UniProtKB:  Q9Y230
GTEx:  ENSG00000183207 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y230
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin-remodeling ATPase INO801,290Homo sapiensMutation(s): 0 
Gene Names: INO80INO80AINOC1KIAA1259
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULG1 (Homo sapiens)
Explore Q9ULG1 
Go to UniProtKB:  Q9ULG1
GTEx:  ENSG00000128908 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULG1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 5607Homo sapiensMutation(s): 0 
Gene Names: ACTR5ARP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9F9 (Homo sapiens)
Explore Q9H9F9 
Go to UniProtKB:  Q9H9F9
PHAROS:  Q9H9F9
GTEx:  ENSG00000101442 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H9F9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
I, M
136Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
J, N
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
K, O
130Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04908
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
L, P
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
INO80 complex subunit BQ [auth R]356Homo sapiensMutation(s): 0 
Gene Names: INO80BHMGA1L4PAPA1ZNHIT4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C086 (Homo sapiens)
Explore Q9C086 
Go to UniProtKB:  Q9C086
GTEx:  ENSG00000115274 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9C086
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (150-MER)R [auth X]228synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains LengthOrganismImage
DNA (150-MER)S [auth Y]228synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



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