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Yorodumi- PDB-9bcu: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -
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-Basic information
Entry | Database: PDB / ID: 9bcu | ||||||
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Title | Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 52 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / 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: 2.2 Å | ||||||
Authors | You, L. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structural basis of archaeal FttA-dependent transcription termination Authors: You, L. / Ebright, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bcu.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9bcu.ent.gz | 793.2 KB | Display | PDB format |
PDBx/mmJSON format | 9bcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/9bcu ftp://data.pdbj.org/pub/pdb/validation_reports/bc/9bcu | HTTPS FTP |
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-Related structure data
Related structure data | 44439MC 9bctC 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) / 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: 16032.955 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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-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 containing 52 nt RNA 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: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48.33 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 977159 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137835 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.09 Å2 | ||||||||||||||||||||||||
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