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 1.1 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:  

  • 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


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 

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