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- PDB-8hyj: A cryo-EM structure of KTF1-bound polymerase V transcription elon... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hyj | |||||||||
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Title | A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex | |||||||||
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![]() | TRANSCRIPTION / Pol V | |||||||||
Function / homology | ![]() : / RNA polymerase IV complex / retrotransposon silencing by siRNA-directed DNA methylation / gene silencing by siRNA-directed DNA methylation / RNA polymerase V complex / : / DSIF complex / regulatory ncRNA-mediated post-transcriptional gene silencing / regulatory ncRNA-mediated gene silencing / siRNA processing ...: / RNA polymerase IV complex / retrotransposon silencing by siRNA-directed DNA methylation / gene silencing by siRNA-directed DNA methylation / RNA polymerase V complex / : / DSIF complex / 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 / transcription by RNA polymerase I / transcription by RNA polymerase III / 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 / heterochromatin formation / RNA polymerase II activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / 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 / nuclear body / protein dimerization activity / nucleotide binding / mRNA binding / chromatin binding / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Zhang, H. / Zhang, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex. Authors: Hong-Wei Zhang / Kun Huang / Zhan-Xi Gu / Xiao-Xian Wu / Jia-Wei Wang / Yu Zhang / ![]() Abstract: De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. ...De novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 729 KB | Display | ![]() |
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PDB format | ![]() | 532.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511 KB | Display | ![]() |
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Full document | ![]() | 564.1 KB | Display | |
Data in XML | ![]() | 71.2 KB | Display | |
Data in CIF | ![]() | 111.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35086MC 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 V subunit ... , 3 types, 3 molecules AEG
#1: Protein | Mass: 218495.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: NRPE1, DMS5, DRD3, NRPD1b, RMD1, RPE1, At2g40030, T28M21.19 Production host: ![]() ![]() |
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#5: Protein | Mass: 25626.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 20287.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases IV and V subunit ... , 3 types, 3 molecules BCD
#2: Protein | Mass: 132848.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 35617.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#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 ... , 5 types, 5 molecules FIJKL
#6: Protein | Mass: 16670.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#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 HW
#8: Protein | Mass: 16533.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#16: Protein | Mass: 158254.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 14926.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#15: DNA chain | Mass: 14643.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules P
#14: RNA chain | Mass: 9492.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 5 molecules ![](data/chem/img/MG.gif)
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#17: Chemical | ChemComp-MG / |
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#18: Chemical | ChemComp-ZN / |
-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: KTF1-bound polymerase V transcription elongation complex Type: COMPLEX / Entity ID: #1-#16 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 608.5 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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
EM software | Name: PHENIX / Version: 1.16_3549: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30359 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 161.95 Å2 | ||||||||||||||||||||||||
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