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- PDB-9k15: A cryo-EM structure of B. oleracea RNA polymerase V in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9k15
TitleA cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom
Components
  • (DNA (34-MER)) x 2
  • (DNA-directed RNA polymerase ...) x 9
  • RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*UP*U)-3')
  • RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein
KeywordsTRANSCRIPTION / DNA-dependent RNA polymerase V / plant
Function / homology
Function and homology information


RNA polymerase IV complex / RNA polymerase V complex / nuclear DNA-directed RNA polymerase complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I ...RNA polymerase IV complex / RNA polymerase V complex / nuclear DNA-directed RNA polymerase complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase I complex / RNA polymerase III complex / transcription elongation by RNA polymerase I / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding
Similarity search - Function
Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 ...Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein / DNA-directed RNA polymerase subunit / Uncharacterized protein / Uncharacterized protein / DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein ...DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein / DNA-directed RNA polymerase subunit / Uncharacterized protein / Uncharacterized protein / DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein / DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesBrassica oleracea (wild cabbage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsXie, G. / Du, X. / Du, J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: EMBO J / Year: 2026
Title: A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.
Authors: Guohui Xie / Xuan Du / Yifang Tan / Yuxing Zhou / Cheng Chi / Sixian Zhou / Colette L Picard / Songge Chai / Lei Wu / Danling Zhu / Jun Zhao / Yan Xue / Sisi Li / Steven E Jacobsen / Zhe Wu / Jiamu Du /
Abstract: DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding ...DNA methylation plays critical roles in eukaryotic gene silencing, genome imprinting, viral defense, and suppression of transposable elements. In plants, RNA Polymerase V (Pol V)-generated non-coding RNA guides DNA methylation through the RNA-directed DNA methylation (RdDM) pathway; however, how these RNAs are selected is unknown. Here, we show that the 3'-ends of Pol V transcripts are enriched at A-rich template DNA (A-rich-DNA). Arabidopsis RdDM regions possess AT-rich boundaries genome-wide, suggesting that Pol V likely terminates at A-rich-DNA, which subsequently defines the DNA methylation landscape in plants. A-rich-DNA successfully stops Pol V transcription in vitro. Structural snapshots of Pol V transcribing A-rich-DNA show that accumulation of unstable rU:dA pairs in the RNA-DNA hybrid promotes transcription bubble collapse and spontaneous transcription termination. These findings identify an intrinsic Pol V termination signal that shapes genomic DNA methylation patterning in plants and reveals a common mechanism for spontaneous transcription termination.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase V largest subunit
C: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
F: DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
J: DNA-directed RNA polymerase II, IV and V subunit 10
K: DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
L: DNA-directed RNA polymerase II, IV and V subunit 12
H: DNA-directed RNA polymerase II, IV and V subunit 8
I: DNA-directed RNA polymerase subunit
E: RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein
B: DNA-directed RNA polymerase IV and V subunit 2
T: DNA (34-MER)
N: DNA (34-MER)
P: RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,81820
Polymers518,40113
Non-polymers4177
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA-directed RNA polymerase ... , 9 types, 9 molecules ACFJKLHIB

#1: Protein DNA-directed RNA polymerase V largest subunit


Mass: 222876.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)
#2: Protein DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein / DNA-directed RNA polymerase II / IV and V subunit 3


Mass: 35484.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3D418
#3: Protein DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein / DNA-directed RNA polymerase V subunit 6


Mass: 16686.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3BZZ8
#4: Protein DNA-directed RNA polymerase II, IV and V subunit 10


Mass: 8167.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3AAT3
#5: Protein DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein / DNA-directed RNA polymerase II / IV and V subunit 11


Mass: 13538.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3DS91
#6: Protein DNA-directed RNA polymerase II, IV and V subunit 12


Mass: 5983.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D2ZPP3
#7: Protein DNA-directed RNA polymerase II, IV and V subunit 8


Mass: 16607.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3DUD8
#8: Protein DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase V subunit 9


Mass: 13123.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3A7P5
#10: Protein DNA-directed RNA polymerase IV and V subunit 2


Mass: 132377.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)

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DNA chain , 2 types, 2 molecules TN

#11: DNA chain DNA (34-MER)


Mass: 10467.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage)
#12: DNA chain DNA (34-MER)


Mass: 10433.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage)

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Protein / RNA chain , 2 types, 2 molecules EP

#13: RNA chain RNA (5'-R(*UP*AP*UP*AP*UP*GP*CP*AP*GP*AP*AP*AP*GP*CP*GP*AP*UP*UP*UP*U)-3')


Mass: 6393.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Brassica oleracea (wild cabbage)
#9: Protein RNA polymerase subunit H/Rpb5 C-terminal domain-containing protein / DNA-directed RNA polymerase V subunit 5


Mass: 26260.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: A0A0D3DTU3

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Non-polymers , 2 types, 7 molecules

#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1DNA-directed RNA polymerase V in complex with 4U scaffoldCOMPLEX#1-#130MULTIPLE SOURCES
2DNA-directed RNA polymerase VCOMPLEX#4-#131NATURAL
3DNA-RNACOMPLEX#1-#31SYNTHETIC
Source (natural)Organism: Brassica oleracea (wild cabbage) / Tissue: inflorescence
Buffer solutionpH: 7.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 280 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.9975 sec. / Electron dose: 1.5625 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3423

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Processing

EM software
IDNameVersionCategory
1RELION3.1.2particle selection
2EPU2.10.0.5RELimage acquisition
4RELION3.1.2CTF correction
7UCSF Chimera1.13.1model fitting
9PHENIX1.17.1model refinement
10RELION3.1.2initial Euler assignment
11RELION3.1.2final Euler assignment
13RELION3.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2295354
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39800 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423812
ELECTRON MICROSCOPYf_angle_d0.56232249
ELECTRON MICROSCOPYf_dihedral_angle_d12.1473492
ELECTRON MICROSCOPYf_chiral_restr0.0433629
ELECTRON MICROSCOPYf_plane_restr0.0044025

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