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Yorodumi- PDB-6fxc: The cryo-EM structure of hibernating 100S ribosome dimer from pat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fxc | |||||||||
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Title | The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus | |||||||||
Components |
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Keywords | RIBOSOME / Ribosome Cryo-EM Structural Biology Hibernation | |||||||||
Function / homology | Function and homology information primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.76 Å | |||||||||
Authors | Matzov, D. / Aibara, S. / Zimmerman, E. / Bashan, A. / Kidmose, R. / Amunts, A. / Yonath, A. | |||||||||
Funding support | Sweden, Israel, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. Authors: Donna Matzov / Shintaro Aibara / Arnab Basu / Ella Zimmerman / Anat Bashan / Mee-Ngan F Yap / Alexey Amunts / Ada E Yonath / Abstract: Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were ...Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient limitation, bacterial ribosomes undergo dimerization, forming a 100S complex that is translationally inactive. Here the authors present the structural basis for formation of the 100S complexes in Gram-positive bacteria, shedding light on the mechanism of translation suppression by the ribosome-silencing factors. | |||||||||
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 | 6fxc.cif.gz | 6.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6fxc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6fxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fxc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6fxc_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6fxc_validation.xml.gz | 386.3 KB | Display | |
Data in CIF | 6fxc_validation.cif.gz | 679.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/6fxc ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fxc | HTTPS FTP |
-Related structure data
Related structure data | 3637MC 3640C 5ngmC 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, 6 molecules AaBaAABAABBB
#1: RNA chain | Mass: 498060.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1248686583 #23: RNA chain | Mass: 946697.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 743649775 #24: RNA chain | Mass: 36974.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1269120188 |
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-30S ribosomal protein ... , 20 types, 40 molecules AbBbAcBcAdBdAeBeAfBfAgBgAhBhAiBiAjBjAkBkAlBlAmBmAnBnAoBoApBp...
#2: Protein | Mass: 25929.135 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXL2 #3: Protein | Mass: 22684.201 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYQ2 #4: Protein | Mass: 22849.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YTH0 #5: Protein | Mass: 16522.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL4 #6: Protein | Mass: 11239.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YVJ2 #7: Protein | Mass: 17181.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VHU6 #8: Protein | Mass: 14723.118 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL1 #9: Protein | Mass: 14312.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1Q4GY48 #10: Protein | Mass: 11009.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYP5 #11: Protein | Mass: 12047.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM1 #12: Protein | Mass: 15075.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PZQ5 #13: Protein | Mass: 13747.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYM0 #14: Protein | Mass: 7186.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYL0 #15: Protein | Mass: 10503.135 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXP3 #16: Protein | Mass: 9993.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YXH8 #17: Protein | Mass: 9366.860 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YYK6 #18: Protein | Mass: 6404.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A1D4K9U8 #19: Protein | Mass: 9205.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133PYC3 #20: Protein | Mass: 8779.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YT41 #21: Protein | Mass: 6241.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YT04 |
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-Protein , 1 types, 2 molecules AvBv
#22: Protein | Mass: 22244.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria) Strain: bovine RF122 / ET3-1 / References: UniProt: Q2YSH7 |
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+50S ribosomal protein ... , 28 types, 56 molecules ACBCADBDAEBEAFBFAGBGAHBHAIBIAJBJAKBKALBLAMBMANBNAOBOAPBPAQBQ...
-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 |
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Molecular weight |
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Source (natural) |
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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: 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 |
Image recording | Electron dose: 2.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 6.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12570 / Num. of class averages: 1 / Symmetry type: POINT |