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Yorodumi- EMDB-12701: CryoEM structure of the transcription termination factor Rho from... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12701 | |||||||||
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Title | CryoEM structure of the transcription termination factor Rho from Mycrobacterium Tuberculosis | |||||||||
Map data | ||||||||||
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 / hydrolase activity / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Martin K / Saridakis E / Vishwakarma R / Lai Kee Him J / Simon I / Cohen-Gonsaud M / Coste F / Margeat E / Boudvillain M / Bron P | |||||||||
Funding support | France, 1 items
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Citation | Journal: Commun Biol / Year: 2022 Title: Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism. Authors: Emmanuel Saridakis / Rishi Vishwakarma / Josephine Lai-Kee-Him / Kevin Martin / Isabelle Simon / Martin Cohen-Gonsaud / Franck Coste / Patrick Bron / Emmanuel Margeat / Marc Boudvillain / Abstract: The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis ...The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [Rho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. To address these issues, we solved the cryo-EM structure of Rho at 3.3 Å resolution. The Rho hexamer is poised into a pre-catalytic, open-ring state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of Rho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency. Our work contributes to explain the unusual features of Rho and provides a framework for future antibiotic development. | |||||||||
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_12701.map.gz | 36.8 MB | EMDB map data format | |
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Header (meta data) | emd-12701-v30.xml emd-12701.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12701_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_12701.png | 58.5 KB | ||
Masks | emd_12701_msk_1.map | 39.5 MB | Mask map | |
Others | emd_12701_additional_1.map.gz emd_12701_half_map_1.map.gz emd_12701_half_map_2.map.gz | 30.3 MB 30.4 MB 30.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12701 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12701 | HTTPS FTP |
-Validation report
Summary document | emd_12701_validation.pdf.gz | 517.4 KB | Display | EMDB validaton report |
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Full document | emd_12701_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | emd_12701_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_12701_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12701 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12701 | HTTPS FTP |
-Related structure data
Related structure data | 7oqhMC 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_12701.map.gz / Format: CCP4 / Size: 39.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.49376 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_12701_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_12701_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12701_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12701_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Transcription termination factor Rho from Mycrobacterium Tuberculosis
Entire | Name: Transcription termination factor Rho from Mycrobacterium Tuberculosis |
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Components |
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-Supramolecule #1: Transcription termination factor Rho from Mycrobacterium Tuberculosis
Supramolecule | Name: Transcription termination factor Rho from Mycrobacterium Tuberculosis type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant cell: Rosette-DE3 / Recombinant plasmid: pET28b |
-Macromolecule #1: Transcription termination factor Rho from Mycrobacterium Tuberculosis
Macromolecule | Name: Transcription termination factor Rho from Mycrobacterium Tuberculosis type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: VVQPVAGILD VLDNYAFVRT SGYLPGPHDV YVSMNMVRKN GMRRGDAVTG AVRVPKEQKF NPLVRLDSIN GGSVEDAKKR PEFGKLTPLY PNQRLRLATS TERLTTRVID LIMPIGKGQR ALIVSPPKAG KTTILQDIAN AITRNNPECH LMVVLVDERP EEVTDMQRSV ...String: VVQPVAGILD VLDNYAFVRT SGYLPGPHDV YVSMNMVRKN GMRRGDAVTG AVRVPKEQKF NPLVRLDSIN GGSVEDAKKR PEFGKLTPLY PNQRLRLATS TERLTTRVID LIMPIGKGQR ALIVSPPKAG KTTILQDIAN AITRNNPECH LMVVLVDERP EEVTDMQRSV KGEVIASTFD RPPSDHTSVA ELAIERAKRL VEQGKDVVVL LDSITRLGRA YNNASPASGR ILSGGVDSTA LYPPKRFLGA ARNIEEGGSL TIIATAMVET GSTGDTVIFE EFKGTGNAEL KLDRKIAERR VFPAVDVNPS GTRKDELLLS PDEFAIVHKL RRVLSGLDSH QAIDLLMSQL RKTKNNYEFL VQVS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.9 Details: 20 mM Tris-Cl 5 % [v/v] glycerol 0.2 mM EDTA 0.2 M KCl 0.2 mM DTT pH 7.9 |
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
Details | Rho (0.5mg/mL) 10uM dC20 oligonucleotide 1mM ATP. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 10888 / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2 Details: The scheme of image recording was made with 7 images per position plus 1 middle, and as a series of 40 frames per movie. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |