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Open data
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Basic information
Entry | Database: PDB / ID: 7bl5 | ||||||||||||
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Title | pre-50S-ObgE particle | ||||||||||||
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![]() | RIBOSOME / pre-50S / ribosome biogenesis / ribosome assembly | ||||||||||||
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 / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / chromosome segregation / response to reactive oxygen species / 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 / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / GDP binding / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Hilal, T. / Nikolay, R. / Spahn, C.M.T. / 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. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 146.1 KB | Display | |
Data in CIF | ![]() | 253.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12218MC ![]() 7bl2C ![]() 7bl3C ![]() 7bl4C ![]() 7bl6C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 29 types, 29 molecules CDEGJLNOQRSTUVWXYZ012IKPMHeFb
-RNA chain , 2 types, 2 molecules BA
#22: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
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#31: RNA chain | Mass: 946433.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() |
-Protein , 4 types, 4 molecules 6789
#26: Protein | Mass: 11594.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0AAT6 |
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#27: Protein | Mass: 37180.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P33643, 23S rRNA pseudouridine1911/1915/1917 synthase |
#28: Protein | Mass: 21395.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0A8X0 |
#29: Protein | Mass: 43340.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
-Non-polymers , 4 types, 31 molecules ![](data/chem/img/GDP.gif)
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![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
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#36: Chemical | ChemComp-GDP / | ||||
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#37: Chemical | #38: Chemical | ChemComp-ZN / | #39: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Assembly intermediate complex 3 / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Cs: 2 mm / C2 aperture diameter: 50 µm |
Image recording | Average exposure time: 5 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 8468 |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 287576 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22282 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 130.13 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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