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- PDB-8xme: Backtracked Pol IV transcription elongation complex -

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Entry
Database: PDB / ID: 8xme
TitleBacktracked Pol IV transcription elongation complex
Components
  • (DNA-directed RNA polymerase IV subunit ...) x 2
  • (DNA-directed RNA polymerases II, IV and V subunit ...) x 7
  • (DNA-directed RNA polymerases IV and V subunit ...) x 2
  • DNA-directed RNA polymerases II and IV subunit 5A
  • Nontemplate_DNA
  • RNA
  • RNA-dependent RNA polymerase 2
  • Template_DNA
KeywordsTRANSCRIPTION/DNA/RNA / elongation / Pol IV / RNA polymerase / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing ...RNA polymerase IV complex / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / plastid / RNA polymerase complex / defense response to fungus / regulation of immune response / heterochromatin / RNA polymerase II, core complex / : / DNA-directed RNA polymerase activity / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase IV/V subunit 1, C-terminal / DNA-directed RNA polymerase IV/V subunit 1, N-terminal / Protein of unknown function (DUF3223) / RDR2 PH-like domain / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon ...DNA-directed RNA polymerase IV/V subunit 1, C-terminal / DNA-directed RNA polymerase IV/V subunit 1, N-terminal / Protein of unknown function (DUF3223) / RDR2 PH-like domain / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / 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 H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / 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. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerases II and IV subunit 5A / RNA-dependent RNA polymerase 2 / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases II, IV and V subunit 3 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A ...DNA / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerases II and IV subunit 5A / RNA-dependent RNA polymerase 2 / DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerases II, IV and V subunit 3 / DNA-directed RNA polymerases IV and V subunit 4 / DNA-directed RNA polymerases II, IV and V subunit 9A / DNA-directed RNA polymerase IV subunit 7 / DNA-directed RNA polymerases II, IV and V subunit 10 / DNA-directed RNA polymerases II, IV and V subunit 6A / DNA-directed RNA polymerases II, IV and V subunit 12 / DNA-directed RNA polymerases IV and V subunit 2 / DNA-directed RNA polymerase IV subunit 1 / DNA-directed RNA polymerases II, IV and V subunit 8B
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang, K. / Fang, C.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2024
Title: Transcription elongation of the plant RNA polymerase IV is prone to backtracking.
Authors: Chengli Fang / Kun Huang / Xiaoxian Wu / Hongwei Zhang / Zhanxi Gu / Jiawei Wang / Yu Zhang /
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- ...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.
History
DepositionDec 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase IV subunit 1
B: DNA-directed RNA polymerases IV and V subunit 2
C: DNA-directed RNA polymerases II, IV and V subunit 3
D: DNA-directed RNA polymerases IV and V subunit 4
E: DNA-directed RNA polymerases II and IV subunit 5A
F: DNA-directed RNA polymerases II, IV and V subunit 6A
G: DNA-directed RNA polymerase IV subunit 7
H: DNA-directed RNA polymerases II, IV and V subunit 8B
I: DNA-directed RNA polymerases II, IV and V subunit 9A
J: DNA-directed RNA polymerases II, IV and V subunit 10
K: DNA-directed RNA polymerases II, IV and V subunit 11
L: DNA-directed RNA polymerases II, IV and V subunit 12
M: RNA-dependent RNA polymerase 2
N: Nontemplate_DNA
O: RNA
Q: Template_DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)638,10426
Polymers637,49116
Non-polymers61310
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 IV subunit ... , 2 types, 2 molecules AG

#1: Protein DNA-directed RNA polymerase IV subunit 1 / DNA-directed RNA polymerase D subunit 1 / AtNRPD1a / Nuclear RNA polymerase D 1a / Protein RNA- ...DNA-directed RNA polymerase D subunit 1 / AtNRPD1a / Nuclear RNA polymerase D 1a / Protein RNA-DIRECTED DNA METHYLATION DEFECTIVE 3 / Protein SILENCING DEFECTIVE 4 / Protein SILENCING MOVEMENT DEFICIENT 2 / RNA polymerase IV subunit 1a / POL IV 1a


Mass: 168101.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: NRPD1, NRPD1a, RMD3, RPD1, SDE4, SMD2, At1g63020, F16M19.19, F16P17.19
Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9LQ02, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase IV subunit 7


Mass: 19873.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LE42

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DNA-directed RNA polymerases IV and V subunit ... , 2 types, 2 molecules BD

#2: Protein DNA-directed RNA polymerases IV and V subunit 2 / DNA-directed RNA polymerase D subunit 2a / AtNRPD2a / Nuclear RNA polymerase D 2a / Nuclear RNA ...DNA-directed RNA polymerase D subunit 2a / AtNRPD2a / Nuclear RNA polymerase D 2a / Nuclear RNA polymerase E 2 / Protein DEFECTIVE IN MERISTEM SILENCING 2 / Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 2 / RNA polymerase IV subunit 2a / POL IV 2a


Mass: 132848.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LK40, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerases IV and V subunit 4 / Protein RNA-DIRECTED DNA METHYLATION 2 / RNA polymerase II / Rpb4 / core protein


Mass: 22447.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6DBA5

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DNA-directed RNA polymerases II, IV and V subunit ... , 7 types, 7 molecules CFHIJKL

#3: Protein DNA-directed RNA polymerases II, IV and V subunit 3 / DNA-directed RNA polymerase II 36 kDa polypeptide A / DNA-directed RNA polymerase II subunit RPB3-A ...DNA-directed RNA polymerase II 36 kDa polypeptide A / DNA-directed RNA polymerase II subunit RPB3-A / RNA polymerase II subunit 3-A / RNA polymerase II subunit B3-A


Mass: 35503.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39211
#6: Protein DNA-directed RNA polymerases II, IV and V subunit 6A / RNA polymerase Rpb6


Mass: 16670.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FJ98
#8: Protein DNA-directed RNA polymerases II, IV and V subunit 8B / RNA polymerase Rpb8


Mass: 16626.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M1A8
#9: Protein DNA-directed RNA polymerases II, IV and V subunit 9A


Mass: 13297.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6NLH0
#10: Protein DNA-directed RNA polymerases II, IV and V subunit 10 / DNA-directed RNA Polymerase II subunit L


Mass: 8323.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LFJ6
#11: Protein DNA-directed RNA polymerases II, IV and V subunit 11 / DNA-directed RNA polymerase II 13.6 kDa polypeptide / DNA-directed RNA polymerase II subunit J / ...DNA-directed RNA polymerase II 13.6 kDa polypeptide / DNA-directed RNA polymerase II subunit J / DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11


Mass: 13582.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q38859
#12: Protein DNA-directed RNA polymerases II, IV and V subunit 12 / DNA-directed RNA Polymerase II subunit K


Mass: 5905.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLM8

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Protein , 2 types, 2 molecules EM

#5: Protein DNA-directed RNA polymerases II and IV subunit 5A / RPB5a / DNA-directed RNA polymerase II subunit E / RNA polymerase I / II and III 24.3 kDa subunit / AtRPB24.3


Mass: 24340.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O81098
#13: Protein RNA-dependent RNA polymerase 2 / AtRDRP2 / Protein SILENCING MOVEMENT DEFICIENT 1 / RNA-directed RNA polymerase 2


Mass: 129494.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O82504, RNA-directed RNA polymerase

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DNA chain , 2 types, 2 molecules NQ

#14: DNA chain Nontemplate_DNA


Mass: 12512.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain Template_DNA


Mass: 12111.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules O

#15: RNA chain RNA


Mass: 5852.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 10 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
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

ComponentName: Backtracked Pol IV transcription elongation complex / Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT
Molecular weightValue: 0.65 kDa/nm / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230158 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00136371
ELECTRON MICROSCOPYf_angle_d0.36949606
ELECTRON MICROSCOPYf_dihedral_angle_d10.42413025
ELECTRON MICROSCOPYf_chiral_restr0.0385767
ELECTRON MICROSCOPYf_plane_restr0.0036108

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