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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11725 | |||||||||||||||
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Title | Transcription termination complex IVa | |||||||||||||||
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![]() | RNA Polymerase / Rho / TRANSCRIPTION | |||||||||||||||
Function / homology | ![]() bacterial-type RNA polymerase core enzyme binding / ATP-dependent activity, acting on RNA / 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 ...bacterial-type RNA polymerase core enzyme binding / ATP-dependent activity, acting on RNA / 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 / translation elongation factor activity / DNA-directed RNA polymerase complex / helicase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / protein complex oligomerization / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / protein domain specific binding / response to antibiotic / nucleotide binding / DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
![]() | Said N / Hilal T / Loll B / Wahl CM / Wahl MC | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ρ. Authors: Nelly Said / Tarek Hilal / Nicholas D Sunday / Ajay Khatri / Jörg Bürger / Thorsten Mielke / Georgiy A Belogurov / Bernhard Loll / Ranjan Sen / Irina Artsimovitch / Markus C Wahl / ![]() ![]() ![]() ![]() Abstract: Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ...Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.8 KB 29.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 93.1 KB | ||
Filedesc metadata | ![]() | 14.3 KB | ||
Others | ![]() | 5.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7adeMC ![]() 6z9pC ![]() 6z9qC ![]() 6z9rC ![]() 6z9sC ![]() 6z9tC ![]() 7adbC ![]() 7adcC ![]() 7addC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_11725_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Transcription termination complex IVa
+Supramolecule #1: Transcription termination complex IVa
+Supramolecule #2: Transcription termination complex IVa
+Supramolecule #3: ntDNA, tDNA and rut RNA
+Macromolecule #1: Transcription termination factor Rho
+Macromolecule #2: Transcription termination/antitermination protein NusA
+Macromolecule #3: DNA-directed RNA polymerase subunit alpha
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: DNA-directed RNA polymerase subunit beta
+Macromolecule #6: DNA-directed RNA polymerase subunit beta'
+Macromolecule #7: tDNA
+Macromolecule #8: ntDNA
+Macromolecule #9: rut RNA
+Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #13: ZINC ION
+Macromolecule #14: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 25.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 31000 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |