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Yorodumi- PDB-6zca: Structure of the B. subtilis RNA POLYMERASE in complex with HelD ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zca | |||||||||||||||||||||
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Title | Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) | |||||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / TRANSCRIPTION/DNA/RNA / DNA-DEPENDENT RNA POLYMERASE / BACTERIAL / Helicase | |||||||||||||||||||||
Function / homology | Function and homology information DNA helicase complex / nucleoid / recombinational repair / 3'-5' DNA helicase activity / DNA helicase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA helicase ...DNA helicase complex / nucleoid / recombinational repair / 3'-5' DNA helicase activity / DNA helicase activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA helicase / protein dimerization activity / hydrolase activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||
Authors | Pei, H.-P. / Hilal, T. / Huang, Y.-H. / Said, N. / Loll, B. / Wahl, M.C. | |||||||||||||||||||||
Funding support | Germany, United States, 6items
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Citation | Journal: Nat Commun / Year: 2020 Title: The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling. Authors: Hao-Hong Pei / Tarek Hilal / Zhuo A Chen / Yong-Heng Huang / Yuan Gao / Nelly Said / Bernhard Loll / Juri Rappsilber / Georgiy A Belogurov / Irina Artsimovitch / Markus C Wahl / Abstract: Cellular RNA polymerases (RNAPs) can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. ...Cellular RNA polymerases (RNAPs) can become trapped on DNA or RNA, threatening genome stability and limiting free enzyme pools, but how RNAP recycling into active states is achieved remains elusive. In Bacillus subtilis, the RNAP δ subunit and NTPase HelD have been implicated in RNAP recycling. We structurally analyzed Bacillus subtilis RNAP-δ-HelD complexes. HelD has two long arms: a Gre cleavage factor-like coiled-coil inserts deep into the RNAP secondary channel, dismantling the active site and displacing RNA, while a unique helical protrusion inserts into the main channel, prying the β and β' subunits apart and, aided by δ, dislodging DNA. RNAP is recycled when, after releasing trapped nucleic acids, HelD dissociates from the enzyme in an ATP-dependent manner. HelD abundance during slow growth and a dimeric (RNAP-δ-HelD) structure that resembles hibernating eukaryotic RNAP I suggest that HelD might also modulate active enzyme pools in response to cellular cues. | |||||||||||||||||||||
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 | 6zca.cif.gz | 643.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zca.ent.gz | 518.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/6zca ftp://data.pdbj.org/pub/pdb/validation_reports/zc/6zca | HTTPS FTP |
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-Related structure data
Related structure data | 11104MC 6zfbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 3 molecules DEH
#1: Protein | Mass: 14914.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: due to weak electron density, we tentatively traced the C-terminal portion of the protein, but could not assign the sequence,due to weak electron density, we tentatively traced the C- ...Details: due to weak electron density, we tentatively traced the C-terminal portion of the protein, but could not assign the sequence,due to weak electron density, we tentatively traced the C-terminal portion of the protein, but could not assign the sequence,due to weak electron density, we tentatively traced the C-terminal portion of the protein, but could not assign the sequence,due to weak electron density, we tentatively traced the C-terminal portion of the protein, but could not assign the sequence Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A0D1KIU7, UniProt: P12464*PLUS |
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#2: Protein | Mass: 8228.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: A0A410WI33, UniProt: O31718*PLUS |
#6: Protein | Mass: 90052.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) References: UniProt: A0A164TSE8, UniProt: O32215*PLUS, DNA helicase |
-DNA-directed RNA polymerase subunit ... , 3 types, 4 molecules UVXY
#3: Protein | Mass: 34842.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) References: UniProt: A0A063XB83, UniProt: P20429*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 133847.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DUE TO LIMITED QUALITY OF THE ELECTRON DENSITY, WE WERE ONLY ABLE TO TRACE SOME OF THE PROTEIN MAIN CHAIN AS POLY-ALA Source: (natural) Bacillus subtilis (bacteria) References: UniProt: A0A2J0WBQ0, UniProt: P37870*PLUS, DNA-directed RNA polymerase #5: Protein | | Mass: 134444.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) References: UniProt: A0A063XB23, UniProt: P37871*PLUS, DNA-directed RNA polymerase |
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-Non-polymers , 1 types, 1 molecules
#7: Chemical | ChemComp-ZN / |
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-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: RNA polymerase in complex with HelD / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Value: 0.46 MDa |
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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 FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Image recording | Average exposure time: 36 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81279 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 4.2 Å / Cross valid method: NONE | ||||||||||||||||||||||||
Refine LS restraints |
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