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- PDB-6zfb: Structure of the B. subtilis RNA POLYMERASE in complex with HelD ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zfb | |||||||||||||||||||||
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Title | Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) | |||||||||||||||||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION/DNA/RNA / DNA-DEPENDENT RNA POLYMERASE / BACTERIAL / Helicase | |||||||||||||||||||||
Function / homology | ![]() DNA helicase complex / nucleoid / recombinational repair / 3'-5' DNA helicase activity / DNA-directed RNA polymerase complex / DNA helicase activity / 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-directed RNA polymerase complex / DNA helicase activity / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||||||||
![]() | Pei, H.-P. / Hilal, T. / Huang, Y.-H. / Said, N. / Loll, B. / Wahl, M.C. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 811 KB | Display | ![]() |
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Full document | ![]() | 828.6 KB | Display | |
Data in XML | ![]() | 165.9 KB | Display | |
Data in CIF | ![]() | 259.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11105MC ![]() 6zcaC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules DdUVuvXxYy
#1: Protein | Mass: 16359.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 34842.387 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A063XB83, UniProt: P20429*PLUS, DNA-directed RNA polymerase #4: Protein | Mass: 133847.938 Da / Num. of mol.: 2 / 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) ![]() ![]() References: UniProt: A0A2J0WBQ0, UniProt: P37870*PLUS, DNA-directed RNA polymerase #5: Protein | Mass: 134444.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A063XB23, UniProt: P37871*PLUS, DNA-directed RNA polymerase |
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-Protein , 2 types, 4 molecules EeHh
#2: Protein | Mass: 8228.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 90052.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A164TSE8, UniProt: O32215*PLUS, DNA helicase |
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-Non-polymers , 1 types, 2 molecules ![](data/chem/img/ZN.gif)
#7: Chemical |
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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 |
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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: 0.9 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176374 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.58 Å2 | ||||||||||||||||||||||||||||
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