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Yorodumi- EMDB-10684: in-cell stalled expressome from pseudouridimycin-treated Mycoplas... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10684 | |||||||||
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Title | in-cell stalled expressome from pseudouridimycin-treated Mycoplasma pneumoniae | |||||||||
Map data | PUM-induced, stalled expressome from Mycoplasma pneumoniae | |||||||||
Sample |
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Biological species | Mycoplasma pneumoniae M129 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Mahamid J / Xue L | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Science / Year: 2020 Title: In-cell architecture of an actively transcribing-translating expressome. Authors: Francis J O'Reilly / Liang Xue / Andrea Graziadei / Ludwig Sinn / Swantje Lenz / Dimitry Tegunov / Cedric Blötz / Neil Singh / Wim J H Hagen / Patrick Cramer / Jörg Stülke / Julia Mahamid ...Authors: Francis J O'Reilly / Liang Xue / Andrea Graziadei / Ludwig Sinn / Swantje Lenz / Dimitry Tegunov / Cedric Blötz / Neil Singh / Wim J H Hagen / Patrick Cramer / Jörg Stülke / Julia Mahamid / Juri Rappsilber / Abstract: Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the ...Structural biology studies performed inside cells can capture molecular machines in action within their native context. In this work, we developed an integrative in-cell structural approach using the genome-reduced human pathogen We combined whole-cell cross-linking mass spectrometry, cellular cryo-electron tomography, and integrative modeling to determine an in-cell architecture of a transcribing and translating expressome at subnanometer resolution. The expressome comprises RNA polymerase (RNAP), the ribosome, and the transcription elongation factors NusG and NusA. We pinpointed NusA at the interface between a NusG-bound elongating RNAP and the ribosome and propose that it can mediate transcription-translation coupling. Translation inhibition dissociated the expressome, whereas transcription inhibition stalled and rearranged it. Thus, the active expressome architecture requires both translation and transcription elongation within the cell. | |||||||||
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_10684.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-10684-v30.xml emd-10684.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10684_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_10684.png | 62.7 KB | ||
Masks | emd_10684_msk_1.map | 30.5 MB | Mask map | |
Others | emd_10684_half_map_1.map.gz emd_10684_half_map_2.map.gz | 23.4 MB 23.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10684 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10684 | HTTPS FTP |
-Related structure data
Related structure data | 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_10684.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PUM-induced, stalled expressome from Mycoplasma pneumoniae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3 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_10684_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: PUM-induced, stalled expressome from Mycoplasma pneumoniae, half 1
File | emd_10684_half_map_1.map | ||||||||||||
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Annotation | PUM-induced, stalled expressome from Mycoplasma pneumoniae, half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: PUM-induced, stalled expressome from Mycoplasma pneumoniae, half 2
File | emd_10684_half_map_2.map | ||||||||||||
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Annotation | PUM-induced, stalled expressome from Mycoplasma pneumoniae, half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : wild-type Mycoplasma pneumoniae M129 cells were treated with 0.4 ...
Entire | Name: wild-type Mycoplasma pneumoniae M129 cells were treated with 0.4 mg/ml pseudouridimycin(PUM), 15-20 minutes prior to blotting and vitrification. |
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Components |
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-Supramolecule #1: wild-type Mycoplasma pneumoniae M129 cells were treated with 0.4 ...
Supramolecule | Name: wild-type Mycoplasma pneumoniae M129 cells were treated with 0.4 mg/ml pseudouridimycin(PUM), 15-20 minutes prior to blotting and vitrification. type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mycoplasma pneumoniae M129 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: modified Hayflick medium as described in Halbedel, Hames, and Stulke 2004, with 0.4 mg/ml pseudouridimycin (PUM) |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 45 % / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.9 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |