9C9T | pdb_00009c9t

S.c INO80 in complex with S.c 0/40 nucleosome, Class 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.

Kaur, U.Wu, H.Cheng, Y.Narlikar, G.J.

(2025) Science 389: eadr3831-eadr3831

  • DOI: https://doi.org/10.1126/science.adr3831
  • Primary Citation of Related Structures:  
    9C9G, 9C9S, 9C9T, 9C9X, 9C9Z, 9CAN, 9CAT, 9CAU, 9CB7, 9CCD

  • PubMed Abstract: 

    Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
136Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HHT1YBR010WYBR0201HHT2SIN2YNL031CN2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P61830 
Go to UniProtKB:  P61830
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61830
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62799
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.1
C, G
132Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTA1H2A1SPT11YDR225WYD9934.10
UniProt
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04911 
Go to UniProtKB:  P04911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04911
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.1
D, H
131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09C
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02293 
Go to UniProtKB:  P02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02293
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin-remodeling ATPase INO80K [auth Q]1,489Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P53115 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53115 
Go to UniProtKB:  P53115
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53115
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 5L [auth R]755Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53946 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53946 
Go to UniProtKB:  P53946
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53946
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Chromatin-remodeling complex subunit IES6M [auth S]166Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32617 
Go to UniProtKB:  P32617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32617
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 1N [auth T],
P [auth V],
R [auth X]
463Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for Q03940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03940 
Go to UniProtKB:  Q03940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03940
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RuvB-like protein 2O [auth U],
Q [auth W],
S [auth Y]
460Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for Q12464 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12464 
Go to UniProtKB:  Q12464
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12464
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ino eighty subunit 2T [auth Z]320Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40154 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40154 
Go to UniProtKB:  P40154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40154
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (227-MER)227synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (227-MER)227synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Database references