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Yorodumi- PDB-5njt: Structure of the Bacillus subtilis hibernating 100S ribosome reve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5njt | ||||||
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Title | Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. | ||||||
Components |
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Keywords | TRANSLATION / 100S / Bacillus subtilis / cryo-EM / Hibernation / HPF / RMF / rRNA / YvyD | ||||||
Function / homology | Function and homology information primary metabolic process / negative regulation of translational elongation / positive regulation of rRNA processing / nucleoid / ribosomal small subunit binding / rRNA processing / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...primary metabolic process / negative regulation of translational elongation / positive regulation of rRNA processing / nucleoid / ribosomal small subunit binding / rRNA processing / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / DNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Beckert, B. / Abdelshahid, M. / Schaefer, H. / Steinchen, W. / Arenz, S. / Berninghausen, O. / Beckmann, R. / Bange, G. / Turgay, K. / Wilson, D.N. | ||||||
Funding support | Germany, 1items
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Citation | Journal: EMBO J / Year: 2017 Title: Structure of the hibernating 100S ribosome reveals the basis for 70S dimerization. Authors: Bertrand Beckert / Maha Abdelshahid / Heinrich Schäfer / Wieland Steinchen / Stefan Arenz / Otto Berninghausen / Roland Beckmann / Gert Bange / Kürşad Turgay / Daniel N Wilson / Abstract: Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ...Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of 100S (100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the hibernating 100S (100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as . | ||||||
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 | 5njt.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5njt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5njt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5njt_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5njt_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5njt_validation.xml.gz | 206.9 KB | Display | |
Data in CIF | 5njt_validation.cif.gz | 362.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/5njt ftp://data.pdbj.org/pub/pdb/validation_reports/nj/5njt | HTTPS FTP |
-Related structure data
Related structure data | 3656MC 3664C 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 , 3 types, 3 molecules AUV
#1: RNA chain | Mass: 500263.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Plasmid details: Bacillus Genetic Stock Center, Columbus, Ohio, USA -1A1 Variant: trpC2 / References: GenBank: 225184640 |
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#21: RNA chain | Mass: 947975.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 467326 |
#22: RNA chain | Mass: 36157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 728882887 |
-30S ribosomal protein ... , 19 types, 19 molecules BCDEFGHIJKLMNOPQRST
#2: Protein | Mass: 25730.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21464 |
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#3: Protein | Mass: 23488.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21465 |
#4: Protein | Mass: 22743.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21466 |
#5: Protein | Mass: 17519.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21467 |
#6: Protein | Mass: 11140.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21468 |
#7: Protein | Mass: 17530.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21469 |
#8: Protein | Mass: 14770.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12879 |
#9: Protein | Mass: 14335.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21470 |
#10: Protein | Mass: 11687.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21471 |
#11: Protein | Mass: 12476.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P04969 |
#12: Protein | Mass: 15117.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21472 |
#13: Protein | Mass: 12599.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P20282 |
#14: Protein | Mass: 7132.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12878 |
#15: Protein | Mass: 10466.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21473 |
#16: Protein | Mass: 10022.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21474 |
#17: Protein | Mass: 10089.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P12874 |
#18: Protein | Mass: 8245.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21475 |
#19: Protein | Mass: 9185.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21476 |
#20: Protein | Mass: 9393.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P21477 |
+50S ribosomal protein ... , 28 types, 28 molecules WXYZabcdefghijklmnopqrstuvwy
-Protein , 1 types, 1 molecules x
#51: Protein | Mass: 12355.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: UniProt: P28368 |
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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: Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization Type: RIBOSOME / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 4 OD260/ml ml Bs100S sample were applied to 2 nm pre-coated Quantifoil R3/3 holey carbon supported grids and vitrified using Vitrobot Mark IV (FEI Company) | ||||||||||||||||||||
Specimen support | Grid type: Quantifoil R3/3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2.5 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 253905 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24546 Details: 30S-70S_subcomplex primary map: 70S-30S_Masked_embf41.mrc Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 276.67 Å2 / Biso mean: 96.7637 Å2 / Biso min: 0 Å2 |