+Open data
-Basic information
Entry | Database: PDB / ID: 8yfe | ||||||
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Title | Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription termination / RNA polymerase II | ||||||
Function / homology | Function and homology information mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA-templated transcription termination / mRNA processing / rRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters ...mRNA 5'-diphosphatase activity / NAD-cap decapping / 5'-3' RNA exonuclease activity / nuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA-templated transcription termination / mRNA processing / rRNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / nucleotide binding / RNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Komagataella phaffii (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||
Authors | Yanagisawa, T. / Murayama, Y. / Ehara, H. / Sekine, S.I. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex. Authors: Tatsuo Yanagisawa / Yuko Murayama / Haruhiko Ehara / Mie Goto / Mari Aoki / Shun-Ichi Sekine / Abstract: The 5´-3´ exoribonuclease Rat1/Xrn2 is responsible for the termination of eukaryotic mRNA transcription by RNAPII. Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a ...The 5´-3´ exoribonuclease Rat1/Xrn2 is responsible for the termination of eukaryotic mRNA transcription by RNAPII. Rat1 forms a complex with its partner proteins, Rai1 and Rtt103, and acts as a "torpedo" to bind transcribing RNAPII and dissociate DNA/RNA from it. Here we report the cryo-electron microscopy structures of the Rat1-Rai1-Rtt103 complex and three Rat1-Rai1-associated RNAPII complexes (type-1, type-1b, and type-2) from the yeast, Komagataella phaffii. The Rat1-Rai1-Rtt103 structure revealed that Rat1 and Rai1 form a heterotetramer with a single Rtt103 bound between two Rai1 molecules. In the type-1 complex, Rat1-Rai1 forms a heterodimer and binds to the RNA exit site of RNAPII to extract RNA into the Rat1 exonuclease active site. This interaction changes the RNA path in favor of termination (the "pre-termination" state). The type-1b and type-2 complexes have no bound DNA/RNA, likely representing the "post-termination" states. These structures illustrate the termination mechanism of eukaryotic mRNA transcription. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yfe.cif.gz | 395.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yfe.ent.gz | 314.4 KB | Display | PDB format |
PDBx/mmJSON format | 8yfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yfe_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8yfe_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8yfe_validation.xml.gz | 63.1 KB | Display | |
Data in CIF | 8yfe_validation.cif.gz | 96.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/8yfe ftp://data.pdbj.org/pub/pdb/validation_reports/yf/8yfe | HTTPS FTP |
-Related structure data
Related structure data | 39221MC 8yf5C 8yfqC 8yfrC 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
#1: Protein | Mass: 115314.461 Da / Num. of mol.: 2 / Mutation: D233A, D235A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: RAT1, PP7435_Chr3-0338 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 References: UniProt: F2QV79, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Protein | Mass: 44595.996 Da / Num. of mol.: 2 / Mutation: E213A, D215A,D233N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Komagataella phaffii (fungus) / Gene: RAI1, PP7435_Chr1-1057 / Production host: Escherichia coli KRX (bacteria) References: UniProt: F2QLF5, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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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: Komagataella phaffii Rat1-Rai1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Komagataella phaffii (fungus) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | 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 | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 75 % / Chamber temperature: 283 K / Details: EMGP2 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1600 nm |
Image recording | Electron dose: 61.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 526250 / Symmetry type: POINT | ||||||||||||||||||||||||
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