9JNW | pdb_00009jnw

Structure of isw1-nucleosome complex in ADP+ state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insights into chromatin remodeling by ISWI during active ATP hydrolysis.

Sia, Y.Pan, H.Chen, K.Chen, Z.

(2025) Science 

  • DOI: https://doi.org/10.1126/science.adu5654
  • Primary Citation of Related Structures:  
    9JNP, 9JNT, 9JNU, 9JNV, 9JNW, 9JNX, 9JNZ, 9JO2, 9JO5, 9LIU, 9LJ2

  • PubMed Abstract: 

    Chromatin remodelers utilize the energy of adenosine triphosphate (ATP) hydrolysis to slide nucleosomes, regulating chromatin structure and gene activity in cells. In this work, we report structures of imitation switch (ISWI) bound to the nucleosome during active ATP hydrolysis and remodeling, revealing conformational transitions of the remodeling motor across the adenosine triphosphatase (ATPase) cycle. The DNA strands are distorted accordingly, showing one full base-pair bulge and a loss of histone contact at the site of motor binding in the adenosine diphosphate* b and Apo* states. We also identify several important elements for regulation of the remodeling activity. Notably, an enzyme conformation exiting the remodeling cycle reveals a linker DNA-sensing brake mechanism. Together, our findings elucidate a multistate model of ISWI action, providing a comprehensive mechanism of DNA translocation and regulation underpinning chromatin remodeling.


  • 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
135Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065LOC108703785LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
Find proteins for A0A8J1LTD2 (Xenopus laevis)
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UniProt GroupA0A8J1LTD2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: LOC494591h2ac14.Lhist1h2ajhist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
122Xenopus laevisMutation(s): 0 
Gene Names: LOC108704303
UniProt
Find proteins for A0A8J0U496 (Xenopus laevis)
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UniProt GroupA0A8J0U496
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ISWI chromatin-remodeling complex ATPase ISW11,061Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ISW1YBR245CYBR1633
EC: 3.6.4
UniProt
Find proteins for P38144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38144
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147Escherichia coli K-12
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references