9JAO | pdb_00009jao

The structure of SMARCAD1 bound to the hexasome in the presence of ADP-BeFx


Experimental Data Snapshot

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

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This is version 1.2 of the entry. See complete history


Literature

Subnucleosome preference of human chromatin remodeller SMARCAD1.

Hu, P.Sun, J.Sun, H.Chen, K.Sia, Y.Xia, X.Xi, Q.Chen, Z.

(2025) Nature 644: 818-826

  • DOI: https://doi.org/10.1038/s41586-025-09100-0
  • Primary Citation of Related Structures:  
    9JAO

  • PubMed Abstract: 

    Chromatin remodellers are pivotal in the regulation of nucleosome dynamics in cells, and they are important for chromatin packaging, transcription, replication and DNA repair 1 . Here we show that the human chromatin remodeller SMARCAD1 exhibits a substrate preference for subnucleosomal particles over the canonical nucleosome. Cryo-electron microscopy structures of SMARCAD1 bound to the nucleosome and hexasome provide mechanistic insights into the substrate selectivity. SMARCAD1 binds to the hexasome through multiple family-specific elements that are essential for the functions in vitro and in cells. The enzyme binds to the canonical nucleosome in an inactive conformation, which accounts for its diminished activity towards the nucleosome. Notably, the histone chaperone FACT complex acts synergistically with H2A-H2B to promote the activity of SMARCAD1 in nucleosome remodelling. Together, our findings reveal an avenue for chromatin regulation, whereby subnucleosomes are remodelled through an ATP-dependent process.


  • Organizational Affiliation
    • MOE Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, P.R. China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1A [auth C],
J [auth K]
845Homo sapiensMutation(s): 0 
Gene Names: SMARCAD1KIAA1122
EC: 3.6.4.12
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PHAROS:  Q9H4L7
GTEx:  ENSG00000163104 
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UniProt GroupQ9H4L7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3B [auth D],
D [auth E]
136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
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Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
E [auth F]
103Xenopus laevisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AF [auth G]130Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.Lh2ac14hist1h2ajLOC494591XELAEV_18003602mg
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1G [auth H]123Xenopus laevisMutation(s): 0 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (157-MER)H [auth I]157synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (157-MER)I [auth J]157synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-03
    Changes: Data collection, Database references