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Yorodumi- EMDB-22115: CryoEM Structure of E. coli Rho-dependent Transcription Pre-termi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22115 | |||||||||
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Title | CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Rho-dependent transcription termination / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information ATP-dependent activity, acting on RNA / transcription elongation-coupled chromatin remodeling / 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 ...ATP-dependent activity, acting on RNA / transcription elongation-coupled chromatin remodeling / 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 / transcription elongation factor complex / regulation of DNA-templated transcription elongation / helicase activity / 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 / protein complex oligomerization / 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 / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Hao ZT / Kim HK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Pre-termination Transcription Complex: Structure and Function. Authors: Zhitai Hao / Vitaly Epshtein / Kelly H Kim / Sergey Proshkin / Vladimir Svetlov / Venu Kamarthapu / Binod Bharati / Alexander Mironov / Thomas Walz / Evgeny Nudler / Abstract: Rho is a general transcription termination factor playing essential roles in RNA polymerase (RNAP) recycling, gene regulation, and genomic stability in most bacteria. Traditional models of ...Rho is a general transcription termination factor playing essential roles in RNA polymerase (RNAP) recycling, gene regulation, and genomic stability in most bacteria. Traditional models of transcription termination postulate that hexameric Rho loads onto RNA prior to contacting RNAP and then translocates along the transcript in pursuit of the moving RNAP to pull RNA from it. Here, we report the cryoelectron microscopy (cryo-EM) structures of two termination process intermediates. Prior to interacting with RNA, Rho forms a specific "pre-termination complex" (PTC) with RNAP and elongation factors NusA and NusG, which stabilize the PTC. RNA exiting RNAP interacts with NusA before entering the central channel of Rho from the distal C-terminal side of the ring. We map the principal interactions in the PTC and demonstrate their critical role in termination. Our results support a mechanism in which the formation of a persistent PTC is a prerequisite for termination. | |||||||||
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_22115.map.gz | 11.2 MB | EMDB map data format | |
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Header (meta data) | emd-22115-v30.xml emd-22115.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22115_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_22115.png | 66.2 KB | ||
Filedesc metadata | emd-22115.cif.gz | 9 KB | ||
Others | emd_22115_additional_1.map.gz | 9.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22115 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22115 | HTTPS FTP |
-Validation report
Summary document | emd_22115_validation.pdf.gz | 371.3 KB | Display | EMDB validaton report |
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Full document | emd_22115_full_validation.pdf.gz | 370.8 KB | Display | |
Data in XML | emd_22115_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_22115_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22115 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22115 | HTTPS FTP |
-Related structure data
Related structure data | 6xavMC 6xasC C: citing same article (ref.) M: atomic model generated by this map |
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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_22115.map.gz / Format: CCP4 / Size: 163.6 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: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: PTC18 composite map
File | emd_22115_additional_1.map | ||||||||||||
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Annotation | PTC18 composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli Rho-dependent Transcription Pre-termination Complex
+Supramolecule #1: E. coli Rho-dependent Transcription Pre-termination Complex
+Macromolecule #1: Transcription termination/antitermination protein NusG
+Macromolecule #5: DNA-directed RNA polymerase subunit omega
+Macromolecule #6: DNA-directed RNA polymerase subunit alpha
+Macromolecule #7: DNA-directed RNA polymerase subunit beta
+Macromolecule #8: DNA-directed RNA polymerase subunit beta'
+Macromolecule #9: Transcription termination/antitermination protein NusA
+Macromolecule #10: Transcription termination factor Rho
+Macromolecule #2: DNA (29-MER)
+Macromolecule #3: DNA (29-MER)
+Macromolecule #4: RNA (18-MER)
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: 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 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6xav: |