[English] 日本語
Yorodumi- PDB-9dr1: E. coli RNA polymerase consensus volume with a bound fluoride rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9dr1 | ||||||
---|---|---|---|---|---|---|---|
Title | E. coli RNA polymerase consensus volume with a bound fluoride riboswitch in the ligand-bound state | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/DNA/RNA / RNA polymerase / riboswitch / fluoride / TRANSFERASE-DNA-RNA complex | ||||||
Function / homology | Function and homology information 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 / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation ...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 / DNA-directed RNA polymerase complex / 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 / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Porta, J.C. / Ellinger, E. / Liu, Y. / Walter, N.G. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural basis of RNA-mediated regulation of transcriptional pausing. Authors: Porta, J.C. / Ellinger, E. / Liu, Y. / Chauvier, A. / Walter, N.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9dr1.cif.gz | 596.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9dr1.ent.gz | 471.3 KB | Display | PDB format |
PDBx/mmJSON format | 9dr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9dr1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9dr1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9dr1_validation.xml.gz | 95.1 KB | Display | |
Data in CIF | 9dr1_validation.cif.gz | 145.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/9dr1 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/9dr1 | HTTPS FTP |
-Related structure data
Related structure data | 47120MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 7942.782 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
---|---|
#2: DNA chain | Mass: 9038.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules GHIJK
#3: Protein | Mass: 25568.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #4: Protein | | Mass: 150560.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase #5: Protein | | Mass: 150436.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, EcE24377A_4529 / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZUK2, DNA-directed RNA polymerase #6: Protein | | Mass: 8963.044 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, Ecok1_36260, APECO1_2812 / Production host: Escherichia coli (E. coli) / References: UniProt: A1AHI0, DNA-directed RNA polymerase |
---|
-RNA chain / Non-polymers , 2 types, 2 molecules R
#7: RNA chain | Mass: 6754.054 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: DNA-directed RNA polymerase |
---|---|
#8: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | Y |
---|---|
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. coli RNA polymerase with a bound fluoride riboswitch in the unliganded state Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.356 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 / Details: 5 mM Tris-HCl, pH 7.5, 100 mM KCl, 1 mM MgCl2 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 5 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: C-flat | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 52.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 419770 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98802 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8G4W Accession code: 8G4W / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|