21VV

Cryo-EM structure of ncBAF bound to the nucleosome

Summary for 21VV

• Entry DOI: 10.2210/pdb21vv/pdb
• EMDB information: 68040
• Descriptor: Histone H3, Actin-like protein 6A, BERYLLIUM TRIFLUORIDE ION, ... (13 entities in total)
• Functional Keywords: chromatin remodeling complex, ncbaf complex, nucleosome, smarca4, bcl7, arp, nuclear protein/dna, nuclear protein-dna complex
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 14
• Total formula weight: 518901.43

Authors

Xu, W.,Cheng, J.,Chen, Y. (deposition date: 2025-12-31, release date: 2026-05-13, Last modification date: 2026-08-12)

Primary citation

Xu, W.,Ma, S.,Li, Y.,Li, M.,Li, C.,Yin, Y.,Li, Q.,Cheng, J.,Chen, Y.
Structural basis of complex assembly and nucleosome recognition by the chromatin remodeling ncBAF complex.
J Mol Cell Biol, 2026

PubMed Abstract: 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.

PubMed: 42377898
DOI: 10.1093/jmcb/mjag020

Experimental method

ELECTRON MICROSCOPY (4.7 Å)