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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12219 | ||||||||||||
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Title | 50S-ObgE-GMPPNP particle | ||||||||||||
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![]() | RIBOSOME / pre-50S / ribosome biogenesis / ribosome assembly | ||||||||||||
Function / homology | ![]() 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 / 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 | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
![]() | Hilal T / Nikolay R | ||||||||||||
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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.3 KB 46.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.3 KB | Display | ![]() |
Images | ![]() | 97.4 KB | ||
Filedesc metadata | ![]() | 10.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 488.2 KB | Display | ![]() |
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Full document | ![]() | 487.7 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bl6MC ![]() 7bl2C ![]() 7bl3C ![]() 7bl4C ![]() 7bl5C 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: 1.74 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 : in vitro reconstituted 50S-ObgE-GMPPNP
+Supramolecule #1: in vitro reconstituted 50S-ObgE-GMPPNP
+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: GTPase ObgE/CgtA
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #29: 23S ribosomal RNA
+Macromolecule #30: 5S ribosomal RNA
+Macromolecule #33: ZINC ION
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #36: 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2179 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7bl6: |