7JIL

70S ribosome Flavobacterium johnsoniae

  • Classification: RIBOSOME
  • Organism(s): Flavobacterium johnsoniae
  • Mutation(s): No 

  • Deposited: 2020-07-23 Released: 2020-12-02 
  • Deposition Author(s): Ortega, J.
  • Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome.

Jha, V.Roy, B.Jahagirdar, D.McNutt, Z.A.Shatoff, E.A.Boleratz, B.L.Watkins, D.E.Bundschuh, R.Basu, K.Ortega, J.Fredrick, K.

(2021) Nucleic Acids Res 49: 547-567

  • DOI: https://doi.org/10.1093/nar/gkaa1195
  • Primary Citation of Related Structures:  
    7JIL

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2A [auth B]274Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1B2U0Q0 (Flavobacterium johnsoniae)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3B [auth C]205Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5L9Q4 (Flavobacterium johnsoniae)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth D]209Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M7D775 (Flavobacterium johnsoniae)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5D [auth E]183Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6E [auth F]180Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5L807 (Flavobacterium johnsoniae)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9F [auth G]146Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5M9Q7 (Flavobacterium johnsoniae)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]151Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5GAA6 (Flavobacterium johnsoniae)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth K]122Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A5FMZ0 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth L]150Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M7D8T3 (Flavobacterium johnsoniae)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16J [auth M]141Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1B2U0I0 (Flavobacterium johnsoniae)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17K [auth N]163Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5L6R0 (Flavobacterium johnsoniae)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18L [auth O]116Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M7D8T4 (Flavobacterium johnsoniae)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19M [auth P]116Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5PX52 (Flavobacterium johnsoniae)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20N [auth Q]114Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1B2U1H3 (Flavobacterium johnsoniae)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21O [auth R]147Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22P [auth S]137Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1B2U0F3 (Flavobacterium johnsoniae)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Q [auth T]96Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1J7BX85 (Flavobacterium johnsoniae)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24R [auth U]104Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1B2U0F5 (Flavobacterium johnsoniae)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25S [auth V]203Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5HDD0 (Flavobacterium johnsoniae)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27T [auth W]86Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M6R2K9 (Flavobacterium johnsoniae)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28U [auth X]78Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1B2U1R1 (Flavobacterium johnsoniae)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29V [auth Y]63Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A5FMZ2 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / BCRC 14874 / CCUG 350202 / NBRC 14942 / NCIMB 11054 / UW101))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30W [auth Z]60Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5L7Z6 (Flavobacterium johnsoniae)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L38AA [auth 4]50Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5JJE6 (Flavobacterium johnsoniae)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S22BA [auth 5]30Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31CA [auth a]84Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth b]64Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1B2U029 (Flavobacterium johnsoniae)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33EA [auth c]60Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1B2U200 (Flavobacterium johnsoniae)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34FA [auth d]53Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1B2U1E7 (Flavobacterium johnsoniae)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35GA [auth e]65Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1J7BZ40 (Flavobacterium johnsoniae)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36HA [auth f]38Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3IA [auth h]252Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4JA [auth i]201Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5KA [auth j]173Flavobacterium johnsoniaeMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6LA [auth k]113Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1J7BSW7 (Flavobacterium johnsoniae)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7MA [auth l]158Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5L9G3 (Flavobacterium johnsoniae)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8NA [auth m]132Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M5L889 (Flavobacterium johnsoniae)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9OA [auth n]128Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1M6R974 (Flavobacterium johnsoniae)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10PA [auth o]101Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1J7CP29 (Flavobacterium johnsoniae)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11QA [auth p]127Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A1J7CBV3 (Flavobacterium johnsoniae)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12RA [auth q]127Flavobacterium johnsoniaeMutation(s): 0 
UniProt
Find proteins for A0A0Q8NJJ8 (Flavobacterium sp. Root186)
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UniProt GroupA0A0Q8NJJ8
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13SA [auth r]124Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14TA [auth s]89Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1B2U0Q7 (Flavobacterium johnsoniae)
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UniProt GroupA0A1B2U0Q7
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15UA [auth t]88Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M6QTP8 (Flavobacterium johnsoniae)
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UniProt GroupA0A1M6QTP8
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16VA [auth u]188Flavobacterium johnsoniaeMutation(s): 0 
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UniProt GroupA0A1M6QGN9
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17WA [auth v]86Flavobacterium johnsoniaeMutation(s): 0 
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Find proteins for A0A1M5L8M4 (Flavobacterium johnsoniae)
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UniProt GroupA0A1M5L8M4
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18XA [auth w]98Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19YA [auth x]92Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20ZA [auth y]83Flavobacterium johnsoniaeMutation(s): 0 
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UniProt GroupA0A1B2U1X2
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21AB [auth z]64Flavobacterium johnsoniaeMutation(s): 0 
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Entity ID: 24
MoleculeChains LengthOrganismImage
RNA (2862-MER)X [auth 1]2,862Flavobacterium johnsoniae
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Entity ID: 25
MoleculeChains LengthOrganismImage
RNA (1519-MER)Y [auth 2]1,520Flavobacterium johnsoniae
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Entity ID: 26
MoleculeChains LengthOrganismImage
RNA (111-MER)Z [auth 3]111Flavobacterium johnsoniae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-12-02 
  • Deposition Author(s): Ortega, J.

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2019-05799

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-01-20
    Changes: Database references
  • Version 2.0: 2021-10-20
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection