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Yorodumi- EMDB-35086: A cryo-EM structure of KTF1-bound polymerase V transcription elon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35086 | |||||||||
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Title | A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pol V / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA polymerase IV complex / : / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / DSIF complex / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / RNA polymerase complex ...RNA polymerase IV complex / : / transposable element silencing by siRNA-mediated heterochromatin formation / RNA polymerase V complex / gene silencing by siRNA-directed DNA methylation / DSIF complex / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / regulatory ncRNA-mediated gene silencing / RNA polymerase complex / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase II activity / regulation of immune response / RNA polymerase I complex / defense response to fungus / RNA polymerase III complex / RNA polymerase II, core complex / heterochromatin / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / heterochromatin formation / 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 / nuclear body / nucleotide binding / mRNA binding / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Zhang H / Zhang Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2023 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35086.map.gz | 55.9 MB | EMDB map data format | |
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Header (meta data) | emd-35086-v30.xml emd-35086.xml | 39.4 KB 39.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35086_fsc.xml emd_35086_fsc_2.xml emd_35086_fsc_3.xml emd_35086_fsc_4.xml | 9.1 KB 8.5 KB 8.5 KB 9.1 KB | Display Display Display Display | FSC data file |
Images | emd_35086.png | 93.3 KB | ||
Filedesc metadata | emd-35086.cif.gz | 10.6 KB | ||
Others | emd_35086_additional_1.map.gz emd_35086_additional_2.map.gz emd_35086_additional_3.map.gz emd_35086_half_map_1.map.gz emd_35086_half_map_2.map.gz | 49.6 MB 1.8 MB 934.8 KB 49.6 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35086 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35086 | HTTPS FTP |
-Validation report
Summary document | emd_35086_validation.pdf.gz | 978 KB | Display | EMDB validaton report |
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Full document | emd_35086_full_validation.pdf.gz | 977.6 KB | Display | |
Data in XML | emd_35086_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_35086_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35086 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35086 | HTTPS FTP |
-Related structure data
Related structure data | 8hyjMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35086.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #3
File | emd_35086_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_35086_additional_2.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_35086_additional_3.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_35086_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_35086_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : KTF1-bound polymerase V transcription elongation complex
+Supramolecule #1: KTF1-bound polymerase V transcription elongation complex
+Macromolecule #1: DNA-directed RNA polymerase V subunit 1
+Macromolecule #2: DNA-directed RNA polymerases IV and V subunit 2
+Macromolecule #3: DNA-directed RNA polymerases IV and V subunit 3B
+Macromolecule #4: DNA-directed RNA polymerases IV and V subunit 4
+Macromolecule #5: DNA-directed RNA polymerase V subunit 5A
+Macromolecule #6: DNA-directed RNA polymerases II, IV and V subunit 6A
+Macromolecule #7: DNA-directed RNA polymerase V subunit 7
+Macromolecule #8: DNA-directed RNA polymerases II and V subunit 8A
+Macromolecule #9: DNA-directed RNA polymerases II, IV and V subunit 9A
+Macromolecule #10: DNA-directed RNA polymerases II, IV and V subunit 10
+Macromolecule #11: DNA-directed RNA polymerases II, IV and V subunit 11
+Macromolecule #12: DNA-directed RNA polymerases II, IV and V subunit 12
+Macromolecule #16: Protein RNA-directed DNA methylation 3
+Macromolecule #13: DNA (48-MER)
+Macromolecule #15: DNA (48-MER)
+Macromolecule #14: RNA (30-MER)
+Macromolecule #17: MAGNESIUM ION
+Macromolecule #18: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |