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TitleStructural basis of complex assembly and nucleosome recognition by the chromatin remodeling ncBAF complex.
Journal, issue, pagesJ Mol Cell Biol, Year 2026
Publish dateJun 30, 2026
AuthorsWancheng Xu / Shengsheng Ma / Yi Li / Muchun Li / Chihang Li / Yue Yin / Qingrun Li / Jingdong Cheng / Yong Chen /
PubMed AbstractBRG1/BRM-associated factor (BAF)-family chromatin remodelers regulate transcription and genome organization by repositioning nucleosomes. The human non-canonical BAF (ncBAF) complex is uniquely ...BRG1/BRM-associated factor (BAF)-family chromatin remodelers regulate transcription and genome organization by repositioning nucleosomes. The human non-canonical BAF (ncBAF) complex is uniquely defined by the presence of BRD9 and GLTSCR1/GLTSCR1L, as well as the absence of the ARID1/2 scaffold and the canonical nucleosome-binding module found in cBAF and PBAF. How ncBAF assembles and engages nucleosomes remains elusive. Here, we present a cryo-EM structure of ncBAF bound to a nucleosome, integrated with biochemical assays and crosslinking mass spectrometry analyses. The ncBAF complex adopts a three-module architecture comprising an ATPase motor module, a repositioned actin-related protein (ARP) module, and a highly flexible Base module. The ncBAF-specific subunits BRD9 and GLTSCR1L are largely dispensable for complex assembly and nucleosome remodeling. Instead, BCL7A directly engages the H2A-H2B acidic patch and the H2A N-terminal tail, providing a structural substitute for SMARCB1 in stimulating remodeling activity. These findings reveal how ncBAF compensates for the loss of the canonical nucleosome-binding module through modular reorganization, providing a structural framework for understanding ncBAF-mediated chromatin regulation and its roles in development and disease.
External linksJ Mol Cell Biol / PubMed:42377898
MethodsEM (single particle)
Resolution3.7 - 4.7 Å
Structure data

68033

21wc

EMDB-68033: CryoEM map of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome
PDB-21wc: Cryo-EM structure of the ATPase domain of SMARCA4 and the finger helix of BCL7A bound to a nucleosome
Method: EM (single particle) / Resolution: 3.9 Å

68034

21wa

EMDB-68034: Cryo-EM map of the ATPase domain of SMARCA4 bound to a nucleosome
PDB-21wa: Cryo-EM structure of the ATPase domain of SMARCA4 bound to a nucleosome
Method: EM (single particle) / Resolution: 3.7 Å

68040

21vv

EMDB-68040, PDB-21vv:
Cryo-EM structure of ncBAF bound to the nucleosome
Method: EM (single particle) / Resolution: 4.7 Å

Chemicals

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • homo sapiens (human)
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
KeywordsNUCLEAR PROTEIN/DNA / Chromatin remodeling complex / ncBAF complex / nucleosome / SMARCA4 / BCL7 / ARP / NUCLEAR PROTEIN-DNA complex / ATPase / NUCLEAR PROTEIN / ncBAF

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