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Yorodumi- PDB-9bct: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -
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-Basic information
Entry | Database: PDB / ID: 9bct | ||||||
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Title | Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase / pre-termination complex / FttA / archaea | ||||||
Function / homology | Function and homology information exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...exonuclease activity / transcription elongation-coupled chromatin remodeling / translation elongation factor activity / DNA-directed RNA polymerase complex / RNA endonuclease activity / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / Hydrolases; Acting on ester bonds / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||
Authors | You, L. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: Structural basis of archaeal FttA-dependent transcription termination. Authors: Linlin You / Chengyuan Wang / Vadim Molodtsov / Konstantin Kuznedelov / Xinyi Miao / Breanna R Wenck / Paul Ulisse / Travis J Sanders / Craig J Marshall / Emre Firlar / Jason T Kaelber / ...Authors: Linlin You / Chengyuan Wang / Vadim Molodtsov / Konstantin Kuznedelov / Xinyi Miao / Breanna R Wenck / Paul Ulisse / Travis J Sanders / Craig J Marshall / Emre Firlar / Jason T Kaelber / Thomas J Santangelo / Richard H Ebright / Abstract: The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre- ...The ribonuclease FttA (also known as aCPSF and aCPSF1) mediates factor-dependent transcription termination in archaea. Here we report the structure of a Thermococcus kodakarensis transcription pre-termination complex comprising FttA, Spt4, Spt5 and a transcription elongation complex (TEC). The structure shows that FttA interacts with the TEC in a manner that enables RNA to proceed directly from the TEC RNA-exit channel to the FttA catalytic centre and that enables endonucleolytic cleavage of RNA by FttA, followed by 5'→3' exonucleolytic cleavage of RNA by FttA and concomitant 5'→3' translocation of FttA on RNA, to apply mechanical force to the TEC and trigger termination. The structure further reveals that Spt5 bridges FttA and the TEC, explaining how Spt5 stimulates FttA-dependent termination. The results reveal functional analogy between bacterial and archaeal factor-dependent termination, functional homology between archaeal and eukaryotic factor-dependent termination, and fundamental mechanistic similarities in factor-dependent termination in bacteria, archaea, and eukaryotes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bct.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9bct.ent.gz | 795.2 KB | Display | PDB format |
PDBx/mmJSON format | 9bct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bct_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 9bct_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 9bct_validation.xml.gz | 123.1 KB | Display | |
Data in CIF | 9bct_validation.cif.gz | 193.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/9bct ftp://data.pdbj.org/pub/pdb/validation_reports/bc/9bct | HTTPS FTP |
-Related structure data
Related structure data | 44438MC 9bcuC 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 subunit ... , 11 types, 11 molecules ABCDEFHKLNP
#1: Protein | Mass: 103038.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE33 |
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#2: Protein | Mass: 127468.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE32 |
#3: Protein | Mass: 43727.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE34, DNA-directed RNA polymerase |
#4: Protein | Mass: 29657.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
#5: Protein | Mass: 21893.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / Strain: TS559 / References: UniProt: Q5JIY4 |
#6: Protein | Mass: 14519.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
#7: Protein | Mass: 9522.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE31, DNA-directed RNA polymerase |
#8: Protein | Mass: 6583.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) |
#9: Protein | Mass: 11013.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JE88, DNA-directed RNA polymerase |
#10: Protein | Mass: 7601.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JJC9, DNA-directed RNA polymerase |
#11: Protein/peptide | Mass: 5553.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermococcus kodakarensis (archaea) / References: UniProt: Q5JDM8, DNA-directed RNA polymerase |
-Transcription elongation factor ... , 2 types, 2 molecules GI
#12: Protein | Mass: 16776.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: spt5 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JH33 |
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#13: Protein | Mass: 8561.870 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: spt4, TK1698 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JIY5 |
-DNA chain , 2 types, 2 molecules 56
#15: DNA chain | Mass: 11096.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#16: DNA chain | Mass: 11060.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 3 molecules JM7
#14: Protein | Mass: 73473.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1428 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5JH24 #17: RNA chain | | Mass: 13649.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 9 molecules
#18: Chemical | ChemComp-MG / |
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#19: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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Has protein modification | N |
-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: FttA-dependent transcription termination complex / Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT |
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Molecular weight | Value: 0.556 MDa / Experimental value: NO |
Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta2 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171269 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.09 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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