8XMD

Pre-translocated Pol IV transcription elongation complex

Summary for 8XMD

• Entry DOI: 10.2210/pdb8xmd/pdb
• EMDB information: 38472
• Descriptor: DNA-directed RNA polymerase IV subunit 1, DNA-directed RNA polymerases II, IV and V subunit 10, DNA-directed RNA polymerases II, IV and V subunit 11, ... (18 entities in total)
• Functional Keywords: transcription/dna/rna, elongation, pol iv, rna polymerase, transcription-dna-rna complex
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 16
• Total formula weight: 629612.38

Authors

Huang, K.,Fang, C.L.,Zhang, Y. (deposition date: 2023-12-27, release date: 2024-07-24, Last modification date: 2025-02-12)

Primary citation

Fang, C.,Huang, K.,Wu, X.,Zhang, H.,Gu, Z.,Wang, J.,Zhang, Y.
Transcription elongation of the plant RNA polymerase IV is prone to backtracking.
Sci Adv, 10:eadq3087-eadq3087, 2024

PubMed Abstract: RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2) to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In the "backtracking-triggered RNA channeling" model, Pol IV backtracks and delivers its transcript's 3' terminus to RDR2, which synthesizes dsRNA. However, the mechanisms underlying Pol IV backtracking and RNA protection from cleavage are unclear. Here, we determined cryo-electron microscopy structures of Pol IV elongation complexes at four states of its nucleotide addition cycle (NAC): posttranslocation, guanosine triphosphate-bound, pretranslocation, and backtracked states. The structures reveal that Pol IV maintains an open DNA cleft and kinked bridge helix in all NAC states, loosely interacts with the nucleoside triphosphate substrate, and barely contacts proximal backtracked nucleotides. Biochemical data indicate that Pol IV is inefficient in forward translocation and RNA cleavage. These findings suggest that Pol IV transcription elongation is prone to backtracking and incapable of RNA hydrolysis, ensuring efficient dsRNA production by Pol IV-RDR2.

PubMed: 39178250
DOI: 10.1126/sciadv.adq3087

Experimental method

ELECTRON MICROSCOPY (3.4 Å)