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Yorodumi- PDB-8jch: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination tran... -
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-Basic information
Entry | Database: PDB / ID: 8jch | |||||||||
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Title | Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 1 (Pol II Rat1-PTTC1) | |||||||||
Components |
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Keywords | TRANSCRIPTION / Transcription termination / Pol II / Rat1/Rai1 / Spt5 | |||||||||
Function / homology | Function and homology information RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity ...RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / termination of RNA polymerase II transcription, poly(A)-coupled / regulation of transcription-coupled nucleotide-excision repair / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / termination of RNA polymerase II transcription, exosome-dependent / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / snRNP binding / regulation of rRNA processing / RNA polymerase I core binding / nucleic acid metabolic process / intracellular mRNA localization / DSIF complex / nuclear mRNA surveillance / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / U4 snRNA binding / : / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process / RNA Polymerase I Transcription Initiation / : / transcription elongation-coupled chromatin remodeling / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase II transcription / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / spliceosomal complex assembly / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / negative regulation of transcription elongation by RNA polymerase II / tRNA transcription by RNA polymerase III / 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 elongation by RNA polymerase I / positive regulation of translational initiation / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / U5 snRNA binding / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / U2 snRNA binding / U6 snRNA binding / enzyme regulator activity / RNA polymerase II, core complex / positive regulation of autophagy / translation initiation factor binding / U1 snRNA binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / rRNA processing / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / single-stranded DNA binding / ribosome biogenesis / chromosome Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Zeng, Y. / Zhang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nature / Year: 2024 Title: Structural basis of exoribonuclease-mediated mRNA transcription termination. Authors: Yuan Zeng / Hong-Wei Zhang / Xiao-Xian Wu / Yu Zhang / Abstract: Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II ...Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II). Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jch.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8jch.ent.gz | 867.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/8jch ftp://data.pdbj.org/pub/pdb/validation_reports/jc/8jch | HTTPS FTP |
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-Related structure data
Related structure data | 36162MC 8k5pC 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 II subunit ... , 7 types, 7 molecules ABCDGIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 143336.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues (1225B-1259B) are an affinity tag(containing a TEV-6xHis-3xFlag tag) we modified in the genome of target strain for convenient protein purification. Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RPB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P16370 |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P20433 |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P34087 |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P27999 |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P38902 |
-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 natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P20434 |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P20435 |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P20436 |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P22139 |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P40422 |
-Protein , 3 types, 3 molecules MOW
#13: Protein | Mass: 117606.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues (1M-13M) are also an affinity tag for convenient protein purification. Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: RAT1, HKE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q02792, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#15: Protein | Mass: 44571.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: RAI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P53063, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
#18: Protein | Mass: 115797.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SPT5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27692 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 14892.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#17: DNA chain | Mass: 14658.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules P
#16: RNA chain | Mass: 7403.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 11 molecules
#19: Chemical | ChemComp-ZN / #20: Chemical | |
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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: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 and Spt5 Type: COMPLEX / Entity ID: #1-#18 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) |
Buffer solution | pH: 7.4 |
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: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 416223 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||
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