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- PDB-8xmd: Pre-translocated Pol IV transcription elongation complex -

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Basic information

Entry
Database: PDB / ID: 8xmd
TitlePre-translocated 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


stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / RNA polymerase V complex / transposable element silencing by siRNA-mediated heterochromatin formation / gene silencing by siRNA-directed DNA methylation / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing ...stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / RNA polymerase V complex / transposable element silencing by siRNA-mediated heterochromatin formation / 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 / RNA polymerase complex / RNA polymerase II activity / regulation of immune response / defense response to fungus / RNA polymerase II, core complex / heterochromatin / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / 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) / 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 / Rpb4/RPC9 superfamily / 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) / 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 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / 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 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, subunit RPB6 / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / 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 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / 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, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / RNA polymerases beta chain signature.
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: 3.4 Å
AuthorsHuang, K. / Fang, C.L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Transcription of the Plant RNA polymerase IV is prone to backtracking
Authors: Huang, K. / Fang, C.L. / Zhang, Y.
History
DepositionDec 27, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)629,61226
Polymers628,99916
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: 6211.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain Template_DNA


Mass: 10571.826 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: 5202.152 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

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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: Pre-translocated 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.: 1.2 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135074 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00136051
ELECTRON MICROSCOPYf_angle_d0.37149119
ELECTRON MICROSCOPYf_dihedral_angle_d10.16812925
ELECTRON MICROSCOPYf_chiral_restr0.0385710
ELECTRON MICROSCOPYf_plane_restr0.0036081

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