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Yorodumi- EMDB-4275: CryoEM structure of E.coli RNA polymerase paused elongation compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4275 | |||||||||
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Title | CryoEM structure of E.coli RNA polymerase paused elongation complex bound to NusA | |||||||||
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Keywords | RNA polymerase / Transcriptional pausing / his pause / NusA / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information 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 / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / protein complex oligomerization ...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 / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / protein complex oligomerization / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / cell motility / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / 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 / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Guo X / Weixlbaumer A | |||||||||
Funding support | France, 1 items
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Citation | Journal: Mol Cell / Year: 2018 Title: Structural Basis for NusA Stabilized Transcriptional Pausing. Authors: Xieyang Guo / Alexander G Myasnikov / James Chen / Corinne Crucifix / Gabor Papai / Maria Takacs / Patrick Schultz / Albert Weixlbaumer / Abstract: Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial ...Transcriptional pausing by RNA polymerases (RNAPs) is a key mechanism to regulate gene expression in all kingdoms of life and is a prerequisite for transcription termination. The essential bacterial transcription factor NusA stimulates both pausing and termination of transcription, thus playing a central role. Here, we report single-particle electron cryo-microscopy reconstructions of NusA bound to paused E. coli RNAP elongation complexes with and without a pause-enhancing hairpin in the RNA exit channel. The structures reveal four interactions between NusA and RNAP that suggest how NusA stimulates RNA folding, pausing, and termination. An asymmetric translocation intermediate of RNA and DNA converts the active site of the enzyme into an inactive state, providing a structural explanation for the inhibition of catalysis. Comparing RNAP at different stages of pausing provides insights on the dynamic nature of the process and the role of NusA as a regulatory factor. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4275.map.gz | 78.7 MB | EMDB map data format | |
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Header (meta data) | emd-4275-v30.xml emd-4275.xml | 34.6 KB 34.6 KB | Display Display | EMDB header |
Images | emd_4275.png | 52.7 KB | ||
Masks | emd_4275_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-4275.cif.gz | 9.3 KB | ||
Others | emd_4275_additional_1.map.gz emd_4275_additional_2.map.gz emd_4275_additional_3.map.gz emd_4275_additional_4.map.gz emd_4275_half_map_1.map.gz emd_4275_half_map_2.map.gz | 78.6 MB 78.7 MB 73.4 MB 78.6 MB 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4275 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4275 | HTTPS FTP |
-Validation report
Summary document | emd_4275_validation.pdf.gz | 275.8 KB | Display | EMDB validaton report |
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Full document | emd_4275_full_validation.pdf.gz | 275 KB | Display | |
Data in XML | emd_4275_validation.xml.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4275 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4275 | HTTPS FTP |
-Related structure data
Related structure data | 6flqMC 4274C 6flpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4275.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4275_msk_1.map | ||||||||||||
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-Additional map: #1
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-Additional map: #2
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-Additional map: #3
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-Additional map: #4
File | emd_4275_additional_4.map | ||||||||||||
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-Supplemental map: emd 4275 half map 1.map
File | emd_4275_half_map_1.map | ||||||||||||
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-Supplemental map: emd 4275 half map 2.map
File | emd_4275_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of E. coli RNA polymerase paused elongation com...
+Supramolecule #1: Cryo-EM structure of E. coli RNA polymerase paused elongation com...
+Supramolecule #2: RNA polymerase, NusA
+Supramolecule #3: Nucleic Acids
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: Transcription termination/antitermination protein NusA
+Macromolecule #6: DNA (31-MER)
+Macromolecule #8: DNA (39-MER)
+Macromolecule #7: RNA (5'-R(*CP*CP*UP*GP*AP*UP*CP*AP*GP*GP*CP*GP*AP*UP*GP*UP*GP*UP*...
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum ER / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-40 / Number real images: 4957 / Average exposure time: 8.0 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6flq: |