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- EMDB-10681: Multibody refinement of 30S ribosome body of Mycoplasma pneumonia... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10681 | |||||||||
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Title | Multibody refinement of 30S ribosome body of Mycoplasma pneumoniae in-cell expressome | |||||||||
![]() | 30S ribosome body of in-cell expressome, multibody refinement | |||||||||
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Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.0 Å | |||||||||
![]() | Mahamid J / Xue L | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.1 KB 15.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 53.5 KB | ||
Masks | ![]() | 30.5 MB | ![]() | |
Others | ![]() ![]() | 22 MB 22 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 30S ribosome body of in-cell expressome, multibody refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.401 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 | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: 30S ribosome body of in-cell expressome, multibody refinement, half 1
File | emd_10681_half_map_1.map | ||||||||||||
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Annotation | 30S ribosome body of in-cell expressome, multibody refinement, half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 30S ribosome body of in-cell expressome, multibody refinement, half2
File | emd_10681_half_map_2.map | ||||||||||||
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Annotation | 30S ribosome body of in-cell expressome, multibody refinement, half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : wild-type Mycoplasma pneumoniae M129 cells
Entire | Name: wild-type Mycoplasma pneumoniae M129 cells |
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Components |
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-Supramolecule #1: wild-type Mycoplasma pneumoniae M129 cells
Supramolecule | Name: wild-type Mycoplasma pneumoniae M129 cells / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 Details: modified Hayflick medium as described in Halbedel, Hames, and Stulke 2004 |
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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 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |