6HTS

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 ...

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RuvB-like 1
A, C, E
456Homo sapiensMutation(s): 0 
Gene Names: RUVBL1 (INO80H, NMP238, TIP49, TIP49A)
EC: 3.6.4.12
Find proteins for Q9Y265 (Homo sapiens)
Go to Gene View: RUVBL1
Go to UniProtKB:  Q9Y265
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RuvB-like 2
B, D, F
463Homo sapiensMutation(s): 0 
Gene Names: RUVBL2 (INO80J, TIP48, TIP49B)
EC: 3.6.4.12
Find proteins for Q9Y230 (Homo sapiens)
Go to Gene View: RUVBL2
Go to UniProtKB:  Q9Y230
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Chromatin-remodeling ATPase INO80
G
1290Homo sapiensMutation(s): 0 
Gene Names: INO80 (INO80A, INOC1, KIAA1259)
EC: 3.6.4.-
Find proteins for Q9ULG1 (Homo sapiens)
Go to Gene View: INO80
Go to UniProtKB:  Q9ULG1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 5
H
607Homo sapiensMutation(s): 0 
Gene Names: ACTR5 (ARP5)
Find proteins for Q9H9F9 (Homo sapiens)
Go to Gene View: ACTR5
Go to UniProtKB:  Q9H9F9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
I, M
136Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Histone H4
J, N
103Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1-B/E
K, O
130Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AC8 (H2AFM, HIST1H2AB, H2AFA, HIST1H2AE)
Find proteins for P04908 (Homo sapiens)
Go to UniProtKB:  P04908
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-J
L, P
126Homo sapiensMutation(s): 0 
Gene Names: H2BC11 (H2BFR, HIST1H2BJ)
Find proteins for P06899 (Homo sapiens)
Go to UniProtKB:  P06899
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
INO80 complex subunit B
R
356Homo sapiensMutation(s): 0 
Gene Names: INO80B (HMGA1L4, PAPA1, ZNHIT4)
Find proteins for Q9C086 (Homo sapiens)
Go to Gene View: INO80B
Go to UniProtKB:  Q9C086
Entity ID: 10
MoleculeChainsLengthOrganism
DNA (150-MER)X228synthetic construct
Entity ID: 11
MoleculeChainsLengthOrganism
DNA (150-MER)Y228synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2018-11-07
    Type: Initial release