9UX9 | pdb_00009ux9

local ATPase-NCP structure of the ncBAF-nucleosome complex in the ADP-BeFx-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for BCL7B-mediated ncBAF-nucleosome engagement.

Sun, F.Zou, B.Li, H.Xu, C.Luo, Q.Wang, C.Xu, P.Pei, D.Chen, J.Qin, D.Zhang, Y.He, J.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkag092
  • Primary Citation of Related Structures:  
    9UX9

  • PubMed Abstract: 

    The mammalian SWI/SNF family of chromatin remodelers comprises BRG1/BRM-associated factor (cBAF), polybromo-associated BAF (PBAF), and non-canonical BAF (ncBAF) complexes, which slide and disassemble nucleosomes to regulate gene expression and chromatin structure dependent on ATP hydrolysis energy. While the chromatin engagement mechanisms of cBAF and PBAF have been structurally resolved, the molecular architecture governing ncBAF interaction with chromatin remains elusive. In this study, by integrating cryo-electron microscopy, biochemical assays, and cross-linking mass spectrometry, we resolved the conformational transition of ncBAF-nucleosome complexes from nucleotide-free to nucleotide-bound states. Our analyses establish BCL7 proteins as dynamic molecular tethers connecting the ARP module to the nucleosomal acidic patch and demonstrate that BCL7B promotes ncBAF-mediated nucleosome remodeling, with BRG1-catalyzed ATP hydrolysis triggering conformational changes that modulate BCL7-mediated histone association. Structurally and biochemically, we further demonstrate that β-actin within the BCL7-containing ARP module retains ATP hydrolysis activity, rendering its exposed pointed end structurally compatible with incorporation into the barbed end of nuclear actin filaments, which provides a potential molecular basis for coordinating nuclear actin networks with chromatin remodeling. Collectively, our findings unravel a dynamic role of BCL7 in regulating ncBAF-mediated chromatin remodeling and establish a distinct chromatin engagement mode of ncBAF from that of cBAF/PBAF.


  • Organizational Affiliation
    • State Key Laboratory of Respiratory Disease, Center for Biomedical Digital Science, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065LOC108703785LOC121398067
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Find proteins for A0A310TTQ1 (Xenopus laevis)
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UniProt GroupA0A310TTQ1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
131Xenopus laevisMutation(s): 0 
Gene Names: LOC494591h2ac14.Lhist1h2ajhist1h2aj.L
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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
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 41,648Homo sapiensMutation(s): 0 
Gene Names: SMARCA4BAF190ABRG1SNF2BSNF2L4
EC: 3.6.4
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Find proteins for P51532 (Homo sapiens)
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PHAROS:  P51532
GTEx:  ENSG00000127616 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (167-MER)167artificial sequences
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (167-MER)167artificial sequences
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32361163669
Other governmentChina2023M743512
National Natural Science Foundation of China (NSFC)China32170189
National Natural Science Foundation of China (NSFC)China32241021
Other governmentChinaGZC20232691
Other governmentChina2023A1515110923

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release