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Yorodumi- EMDB-16299: Structure of yeast RNA Polymerase III elongation complex at 3.3 A -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16299 | |||||||||||||||||||||
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Title | Structure of yeast RNA Polymerase III elongation complex at 3.3 A | |||||||||||||||||||||
Map data | RNA polymerase III-DNA complex main map | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase II activity / nucleotidyltransferase activity / 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 / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Nguyen PQ / Fernandez-Tornero C | |||||||||||||||||||||
Funding support | European Union, France, Spain, 6 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration. Authors: Phong Quoc Nguyen / Sonia Huecas / Amna Asif-Laidin / Adrián Plaza-Pegueroles / Beatrice Capuzzi / Noé Palmic / Christine Conesa / Joël Acker / Juan Reguera / Pascale Lesage / Carlos Fernández-Tornero / Abstract: The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and ...The yeast Ty1 retrotransposon integrates upstream of genes transcribed by RNA polymerase III (Pol III). Specificity of integration is mediated by an interaction between the Ty1 integrase (IN1) and Pol III, currently uncharacterized at the atomic level. We report cryo-EM structures of Pol III in complex with IN1, revealing a 16-residue segment at the IN1 C-terminus that contacts Pol III subunits AC40 and AC19, an interaction that we validate by in vivo mutational analysis. Binding to IN1 associates with allosteric changes in Pol III that may affect its transcriptional activity. The C-terminal domain of subunit C11, involved in RNA cleavage, inserts into the Pol III funnel pore, providing evidence for a two-metal mechanism during RNA cleavage. Additionally, ordering next to C11 of an N-terminal portion from subunit C53 may explain the connection between these subunits during termination and reinitiation. Deletion of the C53 N-terminal region leads to reduced chromatin association of Pol III and IN1, and a major fall in Ty1 integration events. Our data support a model in which IN1 binding induces a Pol III configuration that may favor its retention on chromatin, thereby improving the likelihood of Ty1 integration. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16299.map.gz | 450.5 MB | EMDB map data format | |
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Header (meta data) | emd-16299-v30.xml emd-16299.xml | 42 KB 42 KB | Display Display | EMDB header |
Images | emd_16299.png | 33.1 KB | ||
Others | emd_16299_half_map_1.map.gz emd_16299_half_map_2.map.gz | 442.2 MB 442.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16299 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16299 | HTTPS FTP |
-Validation report
Summary document | emd_16299_validation.pdf.gz | 957.1 KB | Display | EMDB validaton report |
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Full document | emd_16299_full_validation.pdf.gz | 956.7 KB | Display | |
Data in XML | emd_16299_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_16299_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16299 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16299 | HTTPS FTP |
-Related structure data
Related structure data | 8bwsMC 7z0hC 7z2zC 7z30C 7z31C C: citing same article (ref.) M: atomic model generated by this map |
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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_16299.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | RNA polymerase III-DNA complex main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: RNA polymerase III-DNA complex half map A
File | emd_16299_half_map_1.map | ||||||||||||
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Annotation | RNA polymerase III-DNA complex half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RNA polymerase III-DNA complex half map B
File | emd_16299_half_map_2.map | ||||||||||||
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Annotation | RNA polymerase III-DNA complex half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of yeast RNA Polymerase III elongation complex at 3.3 A
+Supramolecule #1: Structure of yeast RNA Polymerase III elongation complex at 3.3 A
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #18: Non-template DNA
+Macromolecule #19: Template DNA
+Macromolecule #20: RNA
+Macromolecule #21: ZINC ION
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pent...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.96 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 101928 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |