+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4380 | |||||||||
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Title | 50S ribosomal subunit assembly intermediate state 3 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / : / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Nikolay R / Hilal T / Qin B / Loerke J / Buerger J / Mielke T / Spahn CMT | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Mol Cell / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4380.map.gz | 70.1 MB | EMDB map data format | |
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Header (meta data) | emd-4380-v30.xml emd-4380.xml | 35.6 KB 35.6 KB | Display Display | EMDB header |
Images | emd_4380.png | 116.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4380 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4380 | HTTPS FTP |
-Related structure data
Related structure data | 6gc4MC 4378C 4379C 4381C 4382C 4383C 6gbzC 6gc0C 6gc6C 6gc7C 6gc8C C: citing same article (ref.) M: atomic model generated by this map |
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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_4380.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : 50S ribosomal assembly intermediate state 3
+Supramolecule #1: 50S ribosomal assembly intermediate state 3
+Macromolecule #1: 50S ribosomal protein L25
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L6
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L17
+Macromolecule #11: 50S ribosomal protein L19
+Macromolecule #12: 50S ribosomal protein L20
+Macromolecule #13: 50S ribosomal protein L21
+Macromolecule #14: 50S ribosomal protein L22
+Macromolecule #15: 50S ribosomal protein L23
+Macromolecule #16: 50S ribosomal protein L24
+Macromolecule #17: 50S ribosomal protein L28
+Macromolecule #18: 50S ribosomal protein L29
+Macromolecule #19: 50S ribosomal protein L32
+Macromolecule #20: 50S ribosomal protein L34
+Macromolecule #21: 50S ribosomal protein L18
+Macromolecule #22: 50S ribosomal protein L5
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L9
+Macromolecule #26: 50S ribosomal protein L27
+Macromolecule #2: 23S ribosomal RNA
+Macromolecule #23: 5S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 80645 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 154462 |
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CTF correction | Software - Name: SPIDER (ver. 14) |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: SPIDER (ver. 14) |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER (ver. 14) / Number images used: 26665 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6gc4: |