8XVS

RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei

8XVS の概要

• エントリーDOI: 10.2210/pdb8xvs/pdb
• EMDBエントリー: 38717
• 分子名称: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC5, DNA-directed RNA polymerase II subunit RPB11-a, ... (21 entities in total)
• 機能のキーワード: rna polymerase, complex, nucleus, nucleosome, transcription-dna-rna complex, transcription/dna/rna
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 23
• 化学式量合計: 733055.93

構造登録者

Kujirai, T.,Kato, J.,Yamamoto, K.,Hirai, S.,Negishi, L.,Ogasawara, M.,Takizawa, Y.,Kurumizaka, H. (登録日: 2024-01-15, 公開日: 2025-05-07, 最終更新日: 2025-06-11)

主引用文献

Kujirai, T.,Kato, J.,Yamamoto, K.,Hirai, S.,Fujii, T.,Maehara, K.,Harada, A.,Negishi, L.,Ogasawara, M.,Yamaguchi, Y.,Ohkawa, Y.,Takizawa, Y.,Kurumizaka, H.
Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis.
Nat Commun, 16:4724-4724, 2025

PubMed Abstract: RNA polymerase II (RNAPII) is a central transcription enzyme that exists as multiple forms with or without accessory factors, and transcribes the genomic DNA packaged in chromatin. To understand how RNAPII functions in the human genome, we isolate transcribing RNAPII complexes from human nuclei by chromatin immunopurification, and determine the cryo-electron microscopy structures of RNAPII elongation complexes (ECs) associated with genomic DNA in distinct forms, without or with the elongation factors SPT4/5, ELOF1, and SPT6. This ChIP-cryoEM method also reveals the two EC-nucleosome complexes corresponding nucleosome disassembly/reassembly processes. In the structure of EC-downstream nucleosome, EC paused at superhelical location (SHL) -5 in the nucleosome, suggesting that SHL(-5) pausing occurs in a sequence-independent manner during nucleosome disassembly. In the structure of the EC-upstream nucleosome, EC directly contacts the nucleosome through the nucleosomal DNA-RPB4/7 stalk and the H2A-H2B dimer-RPB2 wall interactions, suggesting that EC may be paused during nucleosome reassembly. These representative EC structures transcribing the human genome provide mechanistic insights into understanding RNAPII transcription on chromatin.

PubMed: 40436841
DOI: 10.1038/s41467-025-59580-x

実験手法

ELECTRON MICROSCOPY (4.1 Å)