+Open data
-Basic information
Entry | Database: PDB / ID: 7jil | |||||||||
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Title | 70S ribosome Flavobacterium johnsoniae | |||||||||
Components |
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Keywords | RIBOSOME / Translation Initiation / Protein synthesis / bS21 | |||||||||
Function / homology | Function and homology information ribosomal large subunit assembly / large ribosomal subunit / small ribosomal subunit / transferase activity / 5S rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding Similarity search - Function | |||||||||
Biological species | Flavobacterium johnsoniae (bacteria) Flavobacterium sp. Root186 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Ortega, J. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome. Authors: Vikash Jha / Bappaditya Roy / Dushyant Jahagirdar / Zakkary A McNutt / Elan A Shatoff / Bethany L Boleratz / Dean E Watkins / Ralf Bundschuh / Kaustuv Basu / Joaquin Ortega / Kurt Fredrick / Abstract: Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the ...Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein-bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production. | |||||||||
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 | 7jil.cif.gz | 2.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7jil.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7jil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jil_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7jil_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7jil_validation.xml.gz | 178.7 KB | Display | |
Data in CIF | 7jil_validation.cif.gz | 321.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7jil ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7jil | HTTPS FTP |
-Related structure data
Related structure data | 22345MC 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
+50S ribosomal protein ... , 30 types, 30 molecules BCDEFGJKLMNOPQRSTUVWXYZ4abcdef
-RNA chain , 3 types, 3 molecules 123
#24: RNA chain | Mass: 927297.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) |
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#25: RNA chain | Mass: 491833.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) |
#26: RNA chain | Mass: 35661.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) |
-30S ribosomal protein ... , 20 types, 20 molecules 5hijklmnopqrstuvwxyz
#28: Protein/peptide | Mass: 3696.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A4V2PMH1 |
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#35: Protein | Mass: 27886.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBX1 |
#36: Protein | Mass: 22950.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0J7 |
#37: Protein | Mass: 18206.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0I9 |
#38: Protein | Mass: 13376.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7BSW7 |
#39: Protein | Mass: 18493.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L9G3 |
#40: Protein | Mass: 14652.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L889 |
#41: Protein | Mass: 14464.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6R974 |
#42: Protein | Mass: 11446.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CP29 |
#43: Protein | Mass: 13700.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CBV3 |
#44: Protein | Mass: 14121.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium sp. Root186 (bacteria) / References: UniProt: A0A0Q8NJJ8 |
#45: Protein | Mass: 13734.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) |
#46: Protein | Mass: 10211.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U0Q7 |
#47: Protein | Mass: 10565.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QTP8 |
#48: Protein | Mass: 20106.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M6QGN9 |
#49: Protein | Mass: 10108.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8M4 |
#50: Protein | Mass: 11378.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U6N1 |
#51: Protein | Mass: 10278.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1M5L8S8 |
#52: Protein | Mass: 9442.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1B2U1X2 |
#53: Protein | Mass: 7433.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium johnsoniae (bacteria) / References: UniProt: A0A1J7CKJ9 |
-Non-polymers , 1 types, 1 molecules
#54: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | N |
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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: 70S ribosome Flavobacterium johnsoniae / Type: RIBOSOME / Entity ID: #1-#24, #26-#53 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) |
Buffer solution | pH: 7.4 |
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: 50 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 1314417 |
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 705543 / Symmetry type: POINT |