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Yorodumi- PDB-7z30: Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.... -
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-Basic information
Entry | Database: PDB / ID: 7z30 | |||||||||||||||||||||
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Title | Structure of yeast RNA Polymerase III-Ty1 integrase complex at 2.9 A (focus subunit C11 terminal Zn-ribbon in the funnel pore). | |||||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / targeted DNA integration / Ty1 retrotransposon / Ty1 integrase / RNA 19 polymerase III | |||||||||||||||||||||
Function / homology | Function and homology information transposition / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / ribonuclease H ...transposition / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / ribonuclease H / 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 integration / DNA-directed RNA polymerase / RNA-directed DNA polymerase / peroxisome / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / ribosome biogenesis / single-stranded DNA binding / DNA recombination / transcription by RNA polymerase II / nucleic acid binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Nguyen, P.Q. / Fernandez-Tornero, C. | |||||||||||||||||||||
Funding support | European Union, France, Spain, 6items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z30.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7z30.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z30_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7z30_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7z30_validation.xml.gz | 146.5 KB | Display | |
Data in CIF | 7z30_validation.cif.gz | 221.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z30 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z30 | HTTPS FTP |
-Related structure data
Related structure data | 14469MC 7z0hC 7z2zC 7z31C 8bwsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase III subunit ... , 10 types, 10 molecules ABDGIMNOPQ
#1: Protein | Mass: 162517.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPO31, RPC1, RPC160, YOR116C, O3254, YOR3254C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04051, DNA-directed RNA polymerase |
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#2: Protein | Mass: 129629.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RET1, RPC128, RPC2, YOR207C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22276, DNA-directed RNA polymerase |
#4: Protein | Mass: 18623.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC17, YJL011C, J1349 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P47076 |
#7: Protein | Mass: 24349.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC25, YKL144C, UNF1, YKL1 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P35718 |
#9: Protein | Mass: 12525.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC11, YDR045C, YD9609.01C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q04307 |
#13: Protein | Mass: 32178.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC37, YKR025W / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36121 |
#14: Protein | Mass: 42123.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC53, RPC4, YDL150W, D1557 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P25441 |
#15: Protein | Mass: 74112.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC82, RPC3, YPR190C, P9677.11 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32349 |
#16: Protein | Mass: 36174.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC34, YNR003C, N2031 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32910 |
#17: Protein | Mass: 27752.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC31, ACP2, RPC8, YNL151C, N1769 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P17890 |
-DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#3: Protein | Mass: 37732.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC40, RPC5, YPR110C, P8283.18 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07703 |
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#11: Protein | Mass: 16167.860 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC19, YNL113W, N1937 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P28000 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20434 |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20435 |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20436 |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22139 |
#12: Protein | Mass: 7292.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40422 |
-Protein / Protein/peptide , 2 types, 2 molecules WX
#18: Protein | Mass: 71614.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ty1 integrase, Transposon TyH3 Gag-Pol polyprotein, TY1B Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TY1B, POL, TYB1 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q07163 |
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#19: Protein/peptide | Mass: 1464.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae S288C (yeast) |
-Non-polymers , 3 types, 10 molecules
#20: Chemical | ChemComp-ZN / #21: Chemical | #22: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: Cryo-EM map of the crosslinked RNA Polymerase III-Ty1 integrase complex at 2.9 A (focussing on C11 subunit) Type: COMPLEX / Entity ID: #1-#19 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 2800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 42.45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 643858 / Symmetry type: POINT | ||||||||||||||||||||||||
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