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- EMDB-13278: 70S ribosome with A/P- and P/E-site tRNAs in Mycoplasma pneumonia... -
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Open data
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Basic information
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Title | 70S ribosome with A/P- and P/E-site tRNAs in Mycoplasma pneumoniae cells | |||||||||||||||
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Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.7 Å | |||||||||||||||
![]() | Xue L / Lenz S / Rappsilber J / Mahamid J | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Visualizing translation dynamics at atomic detail inside a bacterial cell. Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid / ![]() ![]() ![]() Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells. #1: ![]() Title: Visualizing translation dynamics at atomic detail inside a bacterial cell Authors: Xue L / Lenz S / Zimmermann-Kogadeeva M / Tegunov D / Cramer P / Bork P / Rappsilber J / Mahamid J | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 69.1 KB 69.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 97.1 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Others | ![]() ![]() | 49.7 MB 49.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7panMC ![]() 7oocC ![]() 7oodC ![]() 7p6zC ![]() 7pahC ![]() 7paiC ![]() 7pajC ![]() 7pakC ![]() 7palC ![]() 7pamC ![]() 7paoC ![]() 7paqC ![]() 7parC ![]() 7pasC ![]() 7patC ![]() 7pauC ![]() 7ph9C ![]() 7phaC ![]() 7phbC ![]() 7phcC ![]() 7pi8C ![]() 7pi9C ![]() 7piaC ![]() 7pibC ![]() 7picC ![]() 7pioC ![]() 7pipC ![]() 7piqC ![]() 7pirC ![]() 7pisC ![]() 7pitC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.7005 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
+Supramolecule #1: Cryo-electron tomograms of untreated Mycoplasma pneumoniae cells
+Macromolecule #1: 50S ribosomal protein L34
+Macromolecule #2: 50S ribosomal protein L35
+Macromolecule #3: 50S ribosomal protein L36
+Macromolecule #4: 30S ribosomal protein S2
+Macromolecule #5: 30S ribosomal protein S3
+Macromolecule #6: 30S ribosomal protein S4
+Macromolecule #7: 30S ribosomal protein S5
+Macromolecule #8: 30S ribosomal protein S6
+Macromolecule #9: 30S ribosomal protein S7
+Macromolecule #10: 30S ribosomal protein S8
+Macromolecule #11: 30S ribosomal protein S9
+Macromolecule #12: 30S ribosomal protein S10
+Macromolecule #13: 30S ribosomal protein S11
+Macromolecule #14: 30S ribosomal protein S12
+Macromolecule #15: 30S ribosomal protein S13
+Macromolecule #16: 30S ribosomal protein S14 type Z
+Macromolecule #17: 30S ribosomal protein S15
+Macromolecule #18: 30S ribosomal protein S16
+Macromolecule #19: 30S ribosomal protein S17
+Macromolecule #20: 30S ribosomal protein S18
+Macromolecule #21: 30S ribosomal protein S19
+Macromolecule #22: 30S ribosomal protein S20
+Macromolecule #23: 30S ribosomal protein S21
+Macromolecule #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L9
+Macromolecule #30: 50S ribosomal protein L10
+Macromolecule #31: 50S ribosomal protein L11
+Macromolecule #32: 50S ribosomal protein L13
+Macromolecule #33: 50S ribosomal protein L14
+Macromolecule #34: 50S ribosomal protein L15
+Macromolecule #35: 50S ribosomal protein L16
+Macromolecule #36: 50S ribosomal protein L17
+Macromolecule #37: 50S ribosomal protein L18
+Macromolecule #38: 50S ribosomal protein L19
+Macromolecule #39: 50S ribosomal protein L20
+Macromolecule #40: 50S ribosomal protein L21
+Macromolecule #41: 50S ribosomal protein L22
+Macromolecule #42: 50S ribosomal protein L23
+Macromolecule #43: 50S ribosomal protein L24
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #47: 50S ribosomal protein L31
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L33 1
+Macromolecule #50: 23S ribosomal RNA
+Macromolecule #51: 5S ribosomal RNA
+Macromolecule #52: 16S ribosomal RNA
+Macromolecule #53: tRNA-Phe
-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 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER Details: back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental chamber. |
Details | Mycoplasma pneumoniae M129 cells grown on gold Quantifoil grids at 37 Celsius before plunge freezing. |
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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: 3.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |