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Yorodumi- PDB-6wvj: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wvj | ||||||
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Title | Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA/RNA / DNA-DEPENDENT RNA POLYMERASE / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) Escherichia coli BL21 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
Authors | Newing, T. / Tolun, G. / Oakley, A.J. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD. Authors: Timothy P Newing / Aaron J Oakley / Michael Miller / Catherine J Dawson / Simon H J Brown / James C Bouwer / Gökhan Tolun / Peter J Lewis / Abstract: In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram- ...In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wvj.cif.gz | 510.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wvj.ent.gz | 405.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/6wvj ftp://data.pdbj.org/pub/pdb/validation_reports/wv/6wvj | HTTPS FTP |
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-Related structure data
Related structure data | 21920MC 6wvkC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-11051 (Title: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex Data size: 2.3 TB Data #1: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDF
#1: Protein | Mass: 34842.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: rpoA, BSU01430 / Plasmid: pNG1256 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20429, DNA-directed RNA polymerase #2: Protein | | Mass: 133847.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: rpoB, A3772_00695, BS16045_00134, ETA10_00685, ETK61_00685, GII79_00680 Plasmid: pNG1256 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A2J0WBQ0, UniProt: P37870*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 134444.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: rpoC, A3772_00700, B4122_1444, B4417_1498, BS16045_00135, ETA10_00690, ETK61_00690, GII79_00685 Plasmid: pNG1256 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A063XB23, UniProt: P37871*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 7766.921 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) Gene: rpoZ, A3772_08560, AMC98_03500, B4122_2750, B4417_3585, BS16045_01675, DFO69_2436, ETA10_08595, ETK61_08870, FIU26_02565, FZC71_02355, GII79_08370, SC09_Contig19orf01098 Plasmid: pNG1256 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A063XI46, UniProt: O35011*PLUS, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules TN
#5: DNA chain | Mass: 5814.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) |
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#7: DNA chain | Mass: 2998.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) |
-RNA chain , 1 types, 1 molecules R
#6: RNA chain | Mass: 2596.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) |
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-Non-polymers , 2 types, 3 molecules
#8: Chemical | #9: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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Sequence details | The authors state that the DNA and RNA sequences were built de novo based on density. |
-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 |
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Molecular weight | Value: 0.344200 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pNG1256 | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 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: 298 K Details: Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification. |
-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 FIELDBright-field microscopy / Calibrated magnification: 59500 X / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9 sec. / Electron dose: 52.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5185 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.18rc3_3805: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 463519 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58854 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.36 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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