ISDA: 9K11

Deposition Date 2024-10-16

Release Date 2026-04-15

Last Version Date 2026-04-15

Entry Detail

PDB ID:

9K11

Keywords:

TRANSCRIPTION

Title:

A cryo-EM structure of B. oleracea RNA polymerase V in complex with 0U scaffold at 2.96 Angstrom

Biological Source:

Source Organism(s):

Brassica oleracea (Taxon ID: 3712)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.96 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase V
Chain IDs:D (auth: A)
Chain Length:2032
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Chain IDs:M (auth: B)
Chain Length:1169
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase R
Chain IDs:E (auth: C)
Chain Length:319
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:RNA polymerase subunit H/Rpb5
Chain IDs:L (auth: E)
Chain Length:230
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase R
Chain IDs:F
Chain Length:144
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Chain IDs:J (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase s
Chain IDs:K (auth: I)
Chain Length:114
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Chain IDs:G (auth: J)
Chain Length:71
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase R
Chain IDs:H (auth: K)
Chain Length:116
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I
Chain IDs:I (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polydeoxyribonucleotide
Molecule:0U nontemplated DNA (34-MER)
Chain IDs:B (auth: N)
Chain Length:34
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*UP*AP*UP*AP*UP*GP*
Chain IDs:C (auth: P)
Chain Length:20
Number of Molecules:1
Biological Source:Brassica oleracea

Polymer Type:polydeoxyribonucleotide
Molecule:0U template DNA (34-mer)
Chain IDs:A (auth: T)
Chain Length:34
Number of Molecules:1
Biological Source:Brassica oleracea

Ligand Molecules

Primary Citation

A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.

Xie, G, Du, X, Tan, Y, Zhou, Y, Chi, C, Zhou, S, Picard, C.L, Chai, S, Wu, L, Zhu, D, Zhao, J, Xue, Y, Li, S, Jacobsen, S.E, Wu, Z, Du, J.Show

Embo J. ? ? ? (2026)

PMID: 41928006 DOI: 10.1038/s44318-026-00763-7

Primary Citation of related structures

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