+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12216 | ||||||||||||
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Title | pre-50S-ObgE particle state 2 | ||||||||||||
Map data | |||||||||||||
Sample |
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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 / translational initiation / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / response to reactive oxygen species / cytosolic ribosome assembly / chromosome segregation / 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 / ribosomal large subunit assembly / GDP binding / ribosome binding / large ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / 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: 3.5 Å | ||||||||||||
Authors | Hilal T / Nikolay R / Spahn CMT | ||||||||||||
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_12216.map.gz | 69.6 MB | EMDB map data format | |
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Header (meta data) | emd-12216-v30.xml emd-12216.xml | 42.9 KB 42.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12216_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_12216.png | 125.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12216 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12216 | HTTPS FTP |
-Related structure data
Related structure data | 7bl3MC 7bl2C 7bl4C 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_12216.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 : ribosomal pre-50S assembly intermediate state 2
+Supramolecule #1: ribosomal pre-50S assembly intermediate state 2
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: GTPase ObgE/CgtA
+Macromolecule #4: 50S ribosomal protein L31
+Macromolecule #5: 50S ribosomal protein L2
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L4
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L15
+Macromolecule #11: 50S ribosomal protein L17
+Macromolecule #12: 50S ribosomal protein L18
+Macromolecule #13: 50S ribosomal protein L20
+Macromolecule #14: 50S ribosomal protein L21
+Macromolecule #15: 50S ribosomal protein L22
+Macromolecule #16: 50S ribosomal protein L23
+Macromolecule #17: 50S ribosomal protein L24
+Macromolecule #18: 50S ribosomal protein L25
+Macromolecule #19: 50S ribosomal protein L27
+Macromolecule #20: 50S ribosomal protein L28
+Macromolecule #21: 50S ribosomal protein L29
+Macromolecule #22: 50S ribosomal protein L30
+Macromolecule #23: 50S ribosomal protein L32
+Macromolecule #24: 50S ribosomal protein L33
+Macromolecule #25: 50S ribosomal protein L34
+Macromolecule #26: 50S ribosomal protein L11
+Macromolecule #27: 50S ribosomal protein L14
+Macromolecule #28: 50S ribosomal protein L19
+Macromolecule #29: Ribosomal silencing factor RsfS
+Macromolecule #30: 50S ribosomal protein L9
+Macromolecule #31: 50S ribosomal protein L5
+Macromolecule #32: ZINC ION
+Macromolecule #33: MAGNESIUM ION
+Macromolecule #34: 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 POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus min: 2.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 0.8 µm / Nominal magnification: 36000 |
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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7bl3: |