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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4382 | |||||||||
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Title | 50S ribosomal subunit assembly intermediate state 1 | |||||||||
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![]() | assembly precursor 48S 50S biogenesis in vitro reconstitution / RIBOSOME | |||||||||
Function / homology | ![]() transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
![]() | Nikolay R / Hilal T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Visualization of the Formation and Activation of the 50S Ribosomal Subunit during In Vitro Reconstitution. Authors: Rainer Nikolay / Tarek Hilal / Bo Qin / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kathrin Textoris-Taube / Knud H Nierhaus / Christian M T Spahn / ![]() Abstract: The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ...The assembly of ribosomal subunits is an essential prerequisite for protein biosynthesis in all domains of life. Although biochemical and biophysical approaches have advanced our understanding of ribosome assembly, our mechanistic comprehension of this process is still limited. Here, we perform an in vitro reconstitution of the Escherichia coli 50S ribosomal subunit. Late reconstitution products were subjected to high-resolution cryo-electron microscopy and multiparticle refinement analysis to reconstruct five distinct precursors of the 50S subunit with 4.3-3.8 Å resolution. These assembly intermediates define a progressive maturation pathway culminating in a late assembly particle, whose structure is more than 96% identical to a mature 50S subunit. Our structures monitor the formation and stabilization of structural elements in a nascent particle in unprecedented detail and identify the maturation of the rRNA-based peptidyl transferase center as the final critical step along the 50S assembly pathway. | |||||||||
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 | ![]() | 69.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.8 KB 31.8 KB | Display Display | ![]() |
Images | ![]() | 84.5 KB | ||
Filedesc metadata | ![]() | 8.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gc7MC ![]() 4378C ![]() 4379C ![]() 4380C ![]() 4381C ![]() 4383C ![]() 6gbzC ![]() 6gc0C ![]() 6gc4C ![]() 6gc6C ![]() 6gc8C C: citing same article ( M: atomic model generated by this map |
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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
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Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : 50S ribosomal subunit assembly intermediate state 1
+Supramolecule #1: 50S ribosomal subunit assembly intermediate state 1
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L13
+Macromolecule #5: 50S ribosomal protein L14
+Macromolecule #6: 50S ribosomal protein L15
+Macromolecule #7: 50S ribosomal protein L17
+Macromolecule #8: 50S ribosomal protein L19
+Macromolecule #9: 50S ribosomal protein L20
+Macromolecule #10: 50S ribosomal protein L21
+Macromolecule #11: 50S ribosomal protein L22
+Macromolecule #12: 50S ribosomal protein L23
+Macromolecule #13: 50S ribosomal protein L24
+Macromolecule #14: 50S ribosomal protein L29
+Macromolecule #15: 50S ribosomal protein L32
+Macromolecule #16: 50S ribosomal protein L34
+Macromolecule #17: 50S ribosomal protein L30
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK I |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-25 / Number real images: 4311 / Average exposure time: 5.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6gc7: |