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- PDB-6ztj: E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ztj | ||||||||||||||||||
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Title | E. coli 70S-RNAP expressome complex in NusG-coupled state (38 nt intervening mRNA) | ||||||||||||||||||
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![]() | GENE REGULATION / Transcription / Translation / Expressome / Ribosome / RNA polymerase | ||||||||||||||||||
Function / homology | ![]() RNA secondary structure unwinding / positive regulation of cytoplasmic translation / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly ...RNA secondary structure unwinding / positive regulation of cytoplasmic translation / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / nitrate assimilation / DNA-directed RNA polymerase complex / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / ribosomal large subunit assembly / transcription antitermination / DNA-templated transcription initiation / response to reactive oxygen species / cell motility / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / single-stranded RNA binding / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
![]() | Webster, M.W. / Takacs, M. / Weixlbaumer, A. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of transcription-translation coupling and collision in bacteria. Authors: Michael William Webster / Maria Takacs / Chengjin Zhu / Vita Vidmar / Ayesha Eduljee / Mo'men Abdelkareem / Albert Weixlbaumer / ![]() Abstract: Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The ...Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The lead ribosome potentially contacts RNA polymerase (RNAP) and forms a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here, we present a series of structures representing uncoupled, coupled, and collided expressome states determined by cryo-electron microscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, which stabilizes an otherwise-variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance channel to the RNAP exit channel. In this collided complex, NusG linkage is no longer possible. These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11418MC ![]() 6ztlC ![]() 6ztmC ![]() 6ztnC ![]() 6ztoC ![]() 6ztpC ![]() 6zu1C 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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Components
-RNA chain , 6 types, 6 molecules AAAVAWAXBABB
#1: RNA chain | Mass: 499888.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#22: RNA chain | Mass: 17060.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#23: RNA chain | Mass: 24832.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#24: RNA chain | Mass: 24751.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#26: RNA chain | Mass: 941820.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+30S ribosomal protein ... , 21 types, 21 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAY
+50S ribosomal protein ... , 31 types, 31 molecules BCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZB1B2B3B4B5B6B7
-DNA chain , 2 types, 2 molecules CNCT
#59: DNA chain | Mass: 12063.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#60: DNA chain | Mass: 11872.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules CACBCCCDCE
#61: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #62: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #63: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #64: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein , 1 types, 1 molecules CF
#65: Protein | Mass: 20502.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 484 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/ZN.gif)
![](data/chem/img/PHE.gif)
![](data/chem/img/ZN.gif)
#66: Chemical | ChemComp-MG / #67: Chemical | ChemComp-PHE / | #68: Chemical | ChemComp-ZN / |
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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
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / 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 defocus max: 3500 nm / Nominal defocus min: 700 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
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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: 387633 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15327 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE |