+Open data
-Basic information
Entry | Database: PDB / ID: 7bl3 | ||||||||||||
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Title | pre-50S-ObgE particle state 2 | ||||||||||||
Components |
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Keywords | RIBOSOME / pre-50S / ribosome biogenesis / ribosome assembly | ||||||||||||
Function / homology | Function and homology information guanyl ribonucleotide binding / dormancy process / 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 ...guanyl ribonucleotide binding / dormancy process / 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 | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Hilal, T. / Nikolay, R. / Spahn, C.M.T. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Mol Cell / Year: 2021 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bl3.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7bl3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bl3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7bl3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7bl3_validation.xml.gz | 161 KB | Display | |
Data in CIF | 7bl3_validation.cif.gz | 263.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7bl3 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7bl3 | HTTPS FTP |
-Related structure data
Related structure data | 12216MC 7bl2C 7bl4C 7bl5C 7bl6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 946433.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 |
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#2: RNA chain | Mass: 38483.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 |
-Protein , 2 types, 2 molecules 9P6
#3: Protein | Mass: 43340.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#29: Protein | Mass: 11594.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P0AAT6 |
+50S ribosomal protein ... , 27 types, 27 molecules bCDEGJLNOQRSTUVWXYZ012IKPHF
-Non-polymers , 3 types, 29 molecules
#32: Chemical | ChemComp-ZN / |
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#33: Chemical | ChemComp-MG / |
#34: 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 |
-Sample preparation
Component | Name: ribosomal pre-50S assembly intermediate state 2 / Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus min: 800 nm / Calibrated defocus min: 2500 nm |
Image recording | Electron dose: 25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23445 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.59 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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