8X1C

Structure of nucleosome-bound SRCAP-C in the ADP-bound state

This is a non-PDB format compatible entry.

Summary for 8X1C

• Entry DOI: 10.2210/pdb8x1c/pdb
• EMDB information: 37990
• Descriptor: Histone H2A type 1-C, RuvB-like 2, Actin, cytoplasmic 1, ... (18 entities in total)
• Functional Keywords: remodeler; srcap; h2a.z, dna binding protein/dna, dna binding protein-dna complex
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 25
• Total formula weight: 1168334.45

Authors

Yu, J.,Wang, Q.,Yu, Z.,Li, W.,Wang, L.,Xu, Y. (deposition date: 2023-11-06, release date: 2024-03-06, Last modification date: 2024-05-29)

Primary citation

Yu, J.,Sui, F.,Gu, F.,Li, W.,Yu, Z.,Wang, Q.,He, S.,Wang, L.,Xu, Y.
Structural insights into histone exchange by human SRCAP complex.
Cell Discov, 10:15-15, 2024

PubMed Abstract: Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeF-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.

PubMed: 38331872
DOI: 10.1038/s41421-023-00640-1

Experimental method

ELECTRON MICROSCOPY (3.2 Å)