+Open data
-Basic information
Entry | Database: PDB / ID: 6p18 | ||||||
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Title | Q21 transcription antitermination complex: loading complex | ||||||
Components |
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Keywords | GENE REGULATION / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antiterminator factor | ||||||
Function / homology | Function and homology information negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly ...negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / 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 / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Phage 21 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Yin, Z. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Structural basis of Q-dependent antitermination. Authors: Zhou Yin / Jason T Kaelber / Richard H Ebright / Abstract: Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding ...Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins. | ||||||
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 | 6p18.cif.gz | 764.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p18.ent.gz | 589.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p18_validation.pdf.gz | 932.1 KB | Display | wwPDB validaton report |
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Full document | 6p18_full_validation.pdf.gz | 954.5 KB | Display | |
Data in XML | 6p18_validation.xml.gz | 99.5 KB | Display | |
Data in CIF | 6p18_validation.cif.gz | 157 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/6p18 ftp://data.pdbj.org/pub/pdb/validation_reports/p1/6p18 | HTTPS FTP |
-Related structure data
Related structure data | 20233MC 6p19C 6p1aC 6p1bC 6p1cC 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 (67-MER) fragment carrying phage-21 pR' promoter and pause element, ... , 2 types, 2 molecules 12
#1: DNA chain | Mass: 20704.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phage 21 (virus) |
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#2: DNA chain | Mass: 20588.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phage 21 (virus) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#3: Protein | Mass: 36558.680 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, pez, phs, sez, b3295, JW3257 / Plasmid: pIA900 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #4: Protein | | Mass: 150820.875 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, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Plasmid: pIA900 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A8V2, DNA-directed RNA polymerase #5: Protein | | Mass: 158314.891 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, tabB, b3988, JW3951 / Plasmid: pIA900 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase #6: 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 / Plasmid: pIA900 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase |
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-Protein , 2 types, 3 molecules FPQ
#7: Protein | Mass: 71842.812 Da / Num. of mol.: 1 / Mutation: R541C, L607P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Plasmid: pIA900 / Production host: Escherichia coli (E. coli) / References: UniProt: P00579 |
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#8: Protein | Mass: 18668.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phage 21 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XJQ6 |
-RNA chain , 1 types, 1 molecules R
#9: RNA chain | Mass: 3626.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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-Non-polymers , 2 types, 3 molecules
#10: Chemical | #11: Chemical | ChemComp-MG / | |
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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: Q21-loading complex / Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT | ||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: UltrAuFoil | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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: 22500 X / Calibrated magnification: 47608 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3010 |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1045380 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150310 / Algorithm: FOURIER SPACE / Num. of class averages: 5 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0.143 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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