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Yorodumi- PDB-6awc: Structure of 30S ribosomal subunit and RNA polymerase complex in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6awc | ||||||||||||
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Title | Structure of 30S ribosomal subunit and RNA polymerase complex in rotated state | ||||||||||||
Components |
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Keywords | RIBOSOME / 30S subunit RNA polymerase complex | ||||||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding ...DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / protein dimerization activity / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / DNA-templated transcription / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å | ||||||||||||
Authors | Demo, G. / Rasouly, A. / Vasilyev, N. / Loveland, A.B. / Diaz-Avalos, R. / Grigorieff, N. / Nudler, E. / Korostelev, A.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Elife / Year: 2017 Title: Structure of RNA polymerase bound to ribosomal 30S subunit. Authors: Gabriel Demo / Aviram Rasouly / Nikita Vasilyev / Vladimir Svetlov / Anna B Loveland / Ruben Diaz-Avalos / Nikolaus Grigorieff / Evgeny Nudler / Andrei A Korostelev / Abstract: In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA ...In bacteria, mRNA transcription and translation are coupled to coordinate optimal gene expression and maintain genome stability. Coupling is thought to involve direct interactions between RNA polymerase (RNAP) and the translational machinery. We present cryo-EM structures of RNAP core bound to the small ribosomal 30S subunit. The complex is stable under cell-like ionic conditions, consistent with functional interaction between RNAP and the 30S subunit. The RNA exit tunnel of RNAP aligns with the Shine-Dalgarno-binding site of the 30S subunit. Ribosomal protein S1 forms a wall of the tunnel between RNAP and the 30S subunit, consistent with its role in directing mRNAs onto the ribosome. The nucleic-acid-binding cleft of RNAP samples distinct conformations, suggesting different functional states during transcription-translation coupling. The architecture of the 30S•RNAP complex provides a structural basis for co-localization of the transcriptional and translational machineries, and inform future mechanistic studies of coupled transcription and translation. | ||||||||||||
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 | 6awc.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6awc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6awc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6awc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6awc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6awc_validation.xml.gz | 183.8 KB | Display | |
Data in CIF | 6awc_validation.cif.gz | 295.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/6awc ftp://data.pdbj.org/pub/pdb/validation_reports/aw/6awc | HTTPS FTP |
-Related structure data
Related structure data | 7015MC 7014C 7016C 6awbC 6awdC 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
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules 0102030405
#2: Protein | Mass: 25339.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, Z4665, ECs4160 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z6, DNA-directed RNA polymerase #3: 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, ECS88_4448 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIX3, DNA-directed RNA polymerase #4: Protein | | Mass: 151537.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, Z5561, ECs4911 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T8, DNA-directed RNA polymerase #5: Protein | | Mass: 6552.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, ECS88_4064 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MFL0, DNA-directed RNA polymerase |
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+30S ribosomal protein ... , 21 types, 21 molecules BEFGHIJKLMNOPQRSTUVWX
-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 |
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Molecular weight | Value: 1.3 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7 Details: 20 mM Tris-HCl, pH 7.0, 100 mM NH4Cl, 10 mM MgCl2, 0.5 mM EDTA, 6 mM BME | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 50 nM 30S, 150 nM RNAP | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K Details: 2.5 uL of 50 nM 30S and 150 nM RNAP was applied to the grid. After a 30 second incubation, the grid was blotted for 5 seconds at blotting power 8. |
-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: 25000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 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: 2527 Details: The average electron dose 40.0 (e-/A2) represents the total dose for one collected movie. |
Image scans | Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 184530 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10090 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 500 / Protocol: OTHER / Space: REAL / Target criteria: Correlation Coefficient |