+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12217 | ||||||||||||
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Title | in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle | ||||||||||||
Map data | |||||||||||||
Sample |
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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 / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...guanyl ribonucleotide binding / dormancy process / negative regulation of ribosome biogenesis / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / ribosomal large subunit binding / 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 / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / chromosome segregation / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / GDP binding / large ribosomal subunit / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / transferase activity / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / 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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (strain K12) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
Authors | Hilal T / Nikolay R | ||||||||||||
Funding support | Germany, 3 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12217.map.gz | 165 MB | EMDB map data format | |
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Header (meta data) | emd-12217-v30.xml emd-12217.xml | 47.8 KB 47.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12217_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_12217.png | 111.1 KB | ||
Filedesc metadata | emd-12217.cif.gz | 10.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12217 | HTTPS FTP |
-Validation report
Summary document | emd_12217_validation.pdf.gz | 637.3 KB | Display | EMDB validaton report |
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Full document | emd_12217_full_validation.pdf.gz | 636.8 KB | Display | |
Data in XML | emd_12217_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_12217_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12217 | HTTPS FTP |
-Related structure data
Related structure data | 7bl4MC 7bl2C 7bl3C 7bl5C 7bl6C M: atomic model generated by this map C: citing same article (ref.) |
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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_12217.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 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 : in vitro reconstituted 50S-RsfS-ObgE-GMPPNP complex
+Supramolecule #1: in vitro reconstituted 50S-RsfS-ObgE-GMPPNP complex
+Macromolecule #1: 50S ribosomal protein L36
+Macromolecule #2: 50S ribosomal protein L2
+Macromolecule #3: 50S ribosomal protein L3
+Macromolecule #4: 50S ribosomal protein L4
+Macromolecule #5: 50S ribosomal protein L5
+Macromolecule #6: 50S ribosomal protein L6
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L15
+Macromolecule #9: 50S ribosomal protein L17
+Macromolecule #10: 50S ribosomal protein L18
+Macromolecule #11: 50S ribosomal protein L20
+Macromolecule #12: 50S ribosomal protein L21
+Macromolecule #13: 50S ribosomal protein L22
+Macromolecule #14: 50S ribosomal protein L23
+Macromolecule #15: 50S ribosomal protein L24
+Macromolecule #16: 50S ribosomal protein L25
+Macromolecule #17: 50S ribosomal protein L27
+Macromolecule #18: 50S ribosomal protein L28
+Macromolecule #19: 50S ribosomal protein L29
+Macromolecule #20: 50S ribosomal protein L30
+Macromolecule #21: 50S ribosomal protein L32
+Macromolecule #22: 50S ribosomal protein L33
+Macromolecule #23: 50S ribosomal protein L34
+Macromolecule #24: 50S ribosomal protein L14
+Macromolecule #25: 50S ribosomal protein L19
+Macromolecule #26: 50S ribosomal protein L16
+Macromolecule #27: 50S ribosomal protein L9
+Macromolecule #28: 50S ribosomal protein L31
+Macromolecule #31: Ribosomal silencing factor RsfS
+Macromolecule #32: GTPase ObgE/CgtA
+Macromolecule #33: 50S ribosomal protein L35
+Macromolecule #29: 23S ribosomal RNA
+Macromolecule #30: 5S ribosomal RNA
+Macromolecule #34: ZINC ION
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #37: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus min: 2.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |