+Open data
-Basic information
Entry | Database: PDB / ID: 7mko | |||||||||
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Title | Escherichia coli RNA polymerase elongation complex | |||||||||
Components |
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Keywords | TRANSCRIPTION/DNA/RNA / RNAP recycling / RapA / Post-Termination Complex / PTC / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex | |||||||||
Function / homology | Function and homology information RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Escherichia coli K-12 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Qayyum, M.Z. / Murakami, K.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Biol Chem / Year: 2021 Title: Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli. Authors: M Zuhaib Qayyum / Vadim Molodtsov / Andrew Renda / Katsuhiko S Murakami / Abstract: After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and ...After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined post-termination complex (PTC), limiting the free RNAP pool and subsequently leading to inefficient transcription. In Escherichia coli, a Swi2/Snf2 family of ATPase called RapA is known to be involved in countering such inefficiency through RNAP recycling; however, the precise mechanism of this recycling is unclear. To better understand its mechanism, here we determined the structures of two sets of E. coli RapA-RNAP complexes, along with the RNAP core enzyme and the elongation complex, using cryo-EM. These structures revealed the large conformational changes of RNAP and RapA upon their association that has been implicated in the hindrance of PTC formation. Our results along with DNA-binding assays reveal that although RapA binds RNAP away from the DNA-binding main channel, its binding can allosterically close the RNAP clamp, thereby preventing its nonspecific DNA binding and PTC formation. Taken together, we propose that RapA acts as a guardian of RNAP by which RapA prevents nonspecific DNA binding of RNAP without affecting the binding of promoter DNA recognition σ factor, thereby enhancing RNAP recycling. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mko.cif.gz | 614.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mko.ent.gz | 473.4 KB | Display | PDB format |
PDBx/mmJSON format | 7mko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mko_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7mko_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7mko_validation.xml.gz | 95.9 KB | Display | |
Data in CIF | 7mko_validation.cif.gz | 146.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/7mko ftp://data.pdbj.org/pub/pdb/validation_reports/mk/7mko | HTTPS FTP |
-Related structure data
Related structure data | 23901MC 7mknC 7mkpC 7mkqC 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
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 26213.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rpoA, FAZ83_23195 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: A0A4S5AL01, DNA-directed RNA polymerase #2: Protein | | Mass: 150590.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rpoB, FAZ83_22375 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: A0A4S4NK82, DNA-directed RNA polymerase #3: Protein | | Mass: 150865.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rpoC, FAZ83_22370 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 References: UniProt: A0A6D2WUT6, DNA-directed RNA polymerase #4: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P0A800, DNA-directed RNA polymerase |
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-DNA chain , 2 types, 2 molecules NT
#5: DNA chain | Mass: 8840.689 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
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#7: DNA chain | Mass: 8813.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
-RNA chain , 1 types, 1 molecules R
#6: RNA chain | Mass: 3625.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
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-Non-polymers , 3 types, 4 molecules
#8: Chemical | ChemComp-MG / | ||
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#9: Chemical | #10: Chemical | ChemComp-2TM / | |
-Details
Has ligand of interest | Y |
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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: Escherichia coli RNA polymerase elongation complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) / Strain: K-12 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256565 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.88 Å2 | ||||||||||||||||||||||||
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