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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12218 | ||||||||||||
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Title | pre-50S-ObgE particle | ||||||||||||
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Function / homology | ![]() 23S rRNA pseudouridine1911/1915/1917 synthase / 23S rRNA pseudouridine(1911/1915/1917) synthase activity / guanyl ribonucleotide binding / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / dormancy process / pseudouridine synthase activity / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding ...23S rRNA pseudouridine1911/1915/1917 synthase / 23S rRNA pseudouridine(1911/1915/1917) synthase activity / guanyl ribonucleotide binding / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / dormancy process / pseudouridine synthase activity / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / chromosome segregation / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to radiation / mRNA 5'-UTR binding / GDP binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Hilal T / Nikolay R / Spahn CMT / Schmidt S | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization. Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya ...Authors: Rainer Nikolay / Tarek Hilal / Sabine Schmidt / Bo Qin / David Schwefel / Carlos H Vieira-Vieira / Thorsten Mielke / Jörg Bürger / Justus Loerke / Kazuaki Amikura / Timo Flügel / Takuya Ueda / Matthias Selbach / Elke Deuerling / Christian M T Spahn / ![]() ![]() Abstract: Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. ...Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes. | ||||||||||||
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 | ![]() | 69.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 47.7 KB 47.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.5 KB | Display | ![]() |
Images | ![]() | 150.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bl5MC ![]() 7bl2C ![]() 7bl3C ![]() 7bl4C ![]() 7bl6C M: atomic model generated by this map 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
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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 : Assembly intermediate complex 3
+Supramolecule #1: Assembly intermediate complex 3
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L6
+Macromolecule #5: 50S ribosomal protein L13
+Macromolecule #6: 50S ribosomal protein L15
+Macromolecule #7: 50S ribosomal protein L17
+Macromolecule #8: 50S ribosomal protein L18
+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 L25
+Macromolecule #15: 50S ribosomal protein L27
+Macromolecule #16: 50S ribosomal protein L28
+Macromolecule #17: 50S ribosomal protein L29
+Macromolecule #18: 50S ribosomal protein L30
+Macromolecule #19: 50S ribosomal protein L32
+Macromolecule #20: 50S ribosomal protein L33
+Macromolecule #21: 50S ribosomal protein L34
+Macromolecule #23: 50S ribosomal protein L11
+Macromolecule #24: 50S ribosomal protein L14
+Macromolecule #25: 50S ribosomal protein L19
+Macromolecule #26: Ribosomal silencing factor RsfS
+Macromolecule #27: Ribosomal large subunit pseudouridine synthase D
+Macromolecule #28: UPF0307 protein YjgA
+Macromolecule #29: GTPase ObgE/CgtA
+Macromolecule #30: 50S ribosomal protein L16
+Macromolecule #32: 50S ribosomal protein L9
+Macromolecule #33: 50S ribosomal protein L10
+Macromolecule #34: 50S ribosomal protein L5
+Macromolecule #35: 50S ribosomal protein L31
+Macromolecule #22: 5S ribosomal RNA
+Macromolecule #31: 23S ribosomal RNA
+Macromolecule #36: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ZINC ION
+Macromolecule #39: water
-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 R2/2 / Material: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK II |
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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: COUNTING / Number grids imaged: 3 / Number real images: 8468 / Average exposure time: 5.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 36000 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |