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Yorodumi- PDB-7eu0: The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eu0 | ||||||
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Title | The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-directed RNA polymerase IV / RNA- dependent RNA polymerase 2 / RNA-directed DNA methylation pathway | ||||||
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 / 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 / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | ||||||
Authors | Fang, C.L. / Wu, X.X. / Huang, K. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Science / Year: 2021 Title: Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Authors: Kun Huang / Xiao-Xian Wu / Cheng-Li Fang / Zhou-Geng Xu / Hong-Wei Zhang / Jian Gao / Chuan-Miao Zhou / Lin-Lin You / Zhan-Xi Gu / Wen-Hui Mu / Yu Feng / Jia-Wei Wang / Yu Zhang / Abstract: DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded ...DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo–electron microscopy structures of the Pol IV–RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV–generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a ‘backtracking-triggered RNA channeling’ mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7eu0.cif.gz | 771 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eu0.ent.gz | 596.7 KB | Display | PDB format |
PDBx/mmJSON format | 7eu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eu0_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7eu0_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7eu0_validation.xml.gz | 111.8 KB | Display | |
Data in CIF | 7eu0_validation.cif.gz | 176.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/7eu0 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eu0 | HTTPS FTP |
-Related structure data
Related structure data | 31305MC 7eu1C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AM
#1: Protein | Mass: 169535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) |
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#11: Protein | 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 |
-DNA-directed RNA polymerases ... , 9 types, 9 molecules BCEFHIJKL
#2: Protein | 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 |
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#3: Protein | Mass: 35503.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39211 |
#4: Protein | Mass: 24340.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O81098 |
#5: Protein | Mass: 16670.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FJ98 |
#6: Protein | Mass: 16626.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9M1A8 |
#7: Protein | Mass: 13297.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q6NLH0 |
#8: Protein | Mass: 8323.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8LFJ6 |
#9: Protein | Mass: 13582.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q38859 |
#10: Protein | Mass: 5905.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FLM8 |
-DNA chain , 2 types, 2 molecules NQ
#12: DNA chain | Mass: 6196.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#14: DNA chain | Mass: 9954.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 2 types, 2 molecules OR
#13: RNA chain | Mass: 12215.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: RNA chain | Mass: 1239.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 10 molecules
#16: Chemical | ChemComp-ZN / #17: Chemical | |
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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 |
-Sample preparation
Component | Name: A. thaliana Pol IV-RDR2 backtracked complex / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.55 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 282.65 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 1.95 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63253 / Symmetry type: POINT |