8XMB image
Deposition Date 2023-12-27
Release Date 2024-07-24
Last Version Date 2025-02-12
Entry Detail
PDB ID:
8XMB
Title:
NTP-bound Pol IV transcription elongation complex
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase IV subunit 1
Gene (Uniprot):NRPD1
Chain IDs:A
Chain Length:1498
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases IV and V subunit 2
Gene (Uniprot):NRPD2
Chain IDs:B
Chain Length:1172
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 3
Gene (Uniprot):NRPB3
Chain IDs:C
Chain Length:319
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases IV and V subunit 4
Gene (Uniprot):NRPD4
Chain IDs:D
Chain Length:205
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II and IV subunit 5A
Gene (Uniprot):NRPB5A
Chain IDs:E
Chain Length:205
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 6A
Gene (Uniprot):NRPB6A
Chain IDs:F
Chain Length:144
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase IV subunit 7
Gene (Uniprot):NRPD7
Chain IDs:G
Chain Length:174
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 8B
Gene (Uniprot):NRPB8B
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 9A
Gene (Uniprot):NRPB9A
Chain IDs:I
Chain Length:114
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 10
Gene (Uniprot):NRPB10
Chain IDs:J
Chain Length:71
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 11
Gene (Uniprot):NRPB11
Chain IDs:K
Chain Length:116
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases II, IV and V subunit 12
Gene (Uniprot):NRPB12
Chain IDs:L
Chain Length:51
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:RNA-dependent RNA polymerase 2
Gene (Uniprot):RDR2
Chain IDs:M
Chain Length:1133
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polydeoxyribonucleotide
Molecule:Nontemplate_DNA
Chain IDs:N
Chain Length:20
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:O
Chain Length:15
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:Template_DNA
Chain IDs:P (auth: Q)
Chain Length:33
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Transcription elongation of the plant RNA polymerase IV is prone to backtracking.
Sci Adv 10 eadq3087 eadq3087 (2024)
PMID: 39178250 DOI: 10.1126/sciadv.adq3087

Abstact

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.

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Primary Citation of related structures