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Open data
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Basic information
Entry | Database: PDB / ID: 8xmc | ||||||
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Title | Post-translocated Pol IV transcription elongation complex | ||||||
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![]() | TRANSCRIPTION/DNA/RNA / elongation / Pol IV / RNA polymerase / TRANSCRIPTION-DNA-RNA complex | ||||||
Function / homology | ![]() : / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / retrotransposon silencing by siRNA-directed DNA methylation / RNA polymerase V complex / nuclear RNA-directed RNA polymerase complex / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding ...: / stomatal complex patterning / siRNA-mediated long-distance post-transcriptional gene silencing / RNA polymerase IV complex / retrotransposon silencing by siRNA-directed DNA methylation / RNA polymerase V complex / nuclear RNA-directed RNA polymerase complex / stomatal complex development / siRNA transcription / DNA/RNA hybrid binding / regulatory ncRNA-mediated post-transcriptional gene silencing / regulatory ncRNA-mediated gene silencing / siRNA processing / RNA polymerase complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / regulation of immune response / RNA polymerase I complex / RNA polymerase III complex / defense response to fungus / transcription-coupled nucleotide-excision repair / heterochromatin / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / 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 / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Huang, K. / Fang, C.L. / Zhang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Transcription of the Plant RNA polymerase IV is prone to backtracking Authors: Huang, K. / Fang, C.L. / Zhang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 935.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 115.3 KB | Display | |
Data in CIF | ![]() | 186.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 38471MC ![]() 8xmbC ![]() 8xmdC ![]() 8xmeC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-DNA-directed RNA polymerase IV subunit ... , 2 types, 2 molecules AG
#1: Protein | Mass: 168101.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NRPD1, NRPD1a, RMD3, RPD1, SDE4, SMD2, At1g63020, F16M19.19, F16P17.19 Production host: ![]() ![]() |
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#7: Protein | Mass: 19873.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases IV and V subunit ... , 2 types, 2 molecules BD
#2: Protein | Mass: 132848.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 22447.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases II, IV and V subunit ... , 7 types, 7 molecules CFHIJKL
#3: Protein | Mass: 35503.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 16670.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 16626.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13297.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 8323.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13582.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 5905.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules EM
#5: Protein | Mass: 24340.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#13: Protein | Mass: 129494.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA chain , 2 types, 2 molecules NQ
#14: DNA chain | Mass: 6211.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#16: DNA chain | Mass: 9938.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules O
#15: RNA chain | Mass: 4794.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 10 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#17: Chemical | ChemComp-ZN / #18: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Post-translocated Pol IV transcription elongation complex Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT |
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Molecular weight | Value: 0.65 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 264833 / Symmetry type: POINT | ||||||||||||||||||||||||
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