7X3W

Cryo-EM structure of ISW1-N1 nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the ISW1a complex bound to the dinucleosome.

Li, L.Chen, K.Sia, Y.Hu, P.Ye, Y.Chen, Z.

(2024) Nat Struct Mol Biol 31: 266-274

  • DOI: https://doi.org/10.1038/s41594-023-01174-6
  • Primary Citation of Related Structures:  
    7X3T, 7X3V, 7X3W, 7X3X

  • PubMed Abstract: 

    Nucleosomes are basic repeating units of chromatin and form regularly spaced arrays in cells. Chromatin remodelers alter the positions of nucleosomes and are vital in regulating chromatin organization and gene expression. Here we report the cryo-EM structure of chromatin remodeler ISW1a complex from Saccharomyces cerevisiae bound to the dinucleosome. Each subunit of the complex recognizes a different nucleosome. The motor subunit binds to the mobile nucleosome and recognizes the acidic patch through two arginine residues, while the DNA-binding module interacts with the entry DNA at the nucleosome edge. This nucleosome-binding mode provides the structural basis for linker DNA sensing of the motor. Notably, the Ioc3 subunit recognizes the disk face of the adjacent nucleosome through interacting with the H4 tail, the acidic patch and the nucleosomal DNA, which plays a role in the spacing activity in vitro and in nucleosome organization and cell fitness in vivo. Together, these findings support the nucleosome spacing activity of ISW1a and add a new mode of nucleosome remodeling in the context of a chromatin environment.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
130Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.Lh2ac14hist1h2aj
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
126Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ISWI chromatin-remodeling complex ATPase ISW11,062Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ISW1
EC: 3.6.4
UniProt
Find proteins for P38144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (146-MER)147synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (146-MER)146synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Database references