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Yorodumi- EMDB-27914: Escherichia coli Rho-dependent transcription pre-termination comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27914 | |||||||||
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Title | Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part | |||||||||
Map data | Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part | |||||||||
Sample |
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Function / homology | Function and homology information ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP hydrolysis activity / RNA binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Molodtsov V / Wang C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis of Rho-dependent transcription termination. Authors: Vadim Molodtsov / Chengyuan Wang / Emre Firlar / Jason T Kaelber / Richard H Ebright / Abstract: Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription- ...Rho is a ring-shaped hexameric ATP-dependent molecular motor. Together with the transcription elongation factor NusG, Rho mediates factor-dependent transcription termination and transcription-translation-coupling quality control in Escherichia coli. Here we report the preparation of complexes that are functional in factor-dependent transcription termination from Rho, NusG, RNA polymerase (RNAP), and synthetic nucleic acid scaffolds, and we report cryogenic electron microscopy structures of the complexes. The structures show that functional factor-dependent pre-termination complexes contain a closed-ring Rho hexamer; have RNA threaded through the central channel of Rho; have 60 nucleotides of RNA interacting sequence-specifically with the exterior of Rho and 6 nucleotides of RNA interacting sequence-specifically with the central channel of Rho; have Rho oriented relative to RNAP such that ATP-dependent translocation by Rho exerts mechanical force on RNAP; and have NusG bridging Rho and RNAP. The results explain five decades of research on Rho and provide a foundation for understanding Rho's function. #1: Journal: Biorxiv / Year: 2022 Title: Structural basis of Rho-dependent transcription termination Authors: Molodtsov V / Wang C / Firlar E / Kaelber JT / Ebright RH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27914.map.gz | 135.8 MB | EMDB map data format | |
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Header (meta data) | emd-27914-v30.xml emd-27914.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
Images | emd_27914.png | 20.7 KB | ||
Others | emd_27914_half_map_1.map.gz emd_27914_half_map_2.map.gz | 146.1 MB 146.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27914 | HTTPS FTP |
-Related structure data
Related structure data | 8e5lMC 8e3fC 8e3hC 8e5kC 8e5oC 8e5pC 8e6wC 8e6xC 8e6zC 8e70C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27914.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.038 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map 1 Escherichia coli Rho-dependent transcription pre-termination complex...
File | emd_27914_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2 Escherichia coli Rho-dependent transcription pre-termination complex...
File | emd_27914_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia coli Rho-dependent transcription pre-termination comp...
Entire | Name: Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part |
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Components |
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-Supramolecule #1: Escherichia coli Rho-dependent transcription pre-termination comp...
Supramolecule | Name: Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RNA with 21 nt long spacer
Macromolecule | Name: RNA with 21 nt long spacer / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 11.99382 KDa |
Sequence | String: AUGUUUUUUU UUUUUUUUUU UUUUGAUUUG GUGAGAGG |
-Macromolecule #2: Transcription termination factor Rho
Macromolecule | Name: Transcription termination factor Rho / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 47.070168 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASPI ...String: MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD GFGFLRSADS SYLAGPDDIY VSPSQIRRF NLRTGDTISG KIRPPKEGER YFALLKVNEV NFDKPENARN KILFENLTPL HANSRLRMER GNGSTEDLTA R VLDLASPI GRGQRGLIVA PPKAGKTMLL QNIAQSIAYN HPDCVLMVLL IDERPEEVTE MQRLVKGEVV ASTFDEPASR HV QVAEMVI EKAKRLVEHK KDVIILLDSI TRLARAYNTV VPASGKVLTG GVDANALHRP KRFFGAARNV EEGGSLTIIA TAL IDTGSK MDEVIYEEFK GTGNMELHLS RKIAEKRVFP AIDYNRSGTR KEELLTTQEE LQKMWILRKI IHPMGEIDAM EFLI NKLAM TKTNDDFFEM MKRS |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: COMMON LINE |
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Final angle assignment | Type: COMMON LINE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31098 |