8FN2

The structure of a 50S ribosomal subunit in the Lyme disease pathogen Borreliella burgdorferi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

The structure of a hibernating ribosome in a Lyme disease pathogen.

Sharma, M.R.Manjari, S.R.Agrawal, E.K.Keshavan, P.Koripella, R.K.Majumdar, S.Marcinkiewicz, A.L.Lin, Y.P.Agrawal, R.K.Banavali, N.K.

(2023) Nat Commun 14: 6961-6961

  • DOI: https://doi.org/10.1038/s41467-023-42266-7
  • Primary Citation of Related Structures:  
    8FMW, 8FN2

  • PubMed Abstract: 

    The spirochete bacterial pathogen Borrelia (Borreliella) burgdorferi (Bbu) affects more than 10% of the world population and causes Lyme disease in about half a million people in the US annually. Therapy for Lyme disease includes antibiotics that target the Bbu ribosome. Here we present the structure of the Bbu 70S ribosome obtained by single particle cryo-electron microscopy at 2.9 Å resolution, revealing a bound hibernation promotion factor protein and two genetically non-annotated ribosomal proteins bS22 and bL38. The ribosomal protein uL30 in Bbu has an N-terminal α-helical extension, partly resembling the mycobacterial bL37 protein, suggesting evolution of bL37 and a shorter uL30 from a longer uL30 protein. Its analogy to proteins uL30m and mL63 in mammalian mitochondrial ribosomes also suggests a plausible evolutionary pathway for expansion of protein content in mammalian mitochondrial ribosomes. Computational binding free energy predictions for antibiotics reflect subtle distinctions in antibiotic-binding sites in the Bbu ribosome. Discovery of these features in the Bbu ribosome may enable better ribosome-targeted antibiotic design for Lyme disease treatment.


  • Organizational Affiliation

    Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth D]277Borreliella burgdorferi B31Mutation(s): 0 
UniProt
Find proteins for P94270 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth E]206Borreliella burgdorferi B31Mutation(s): 0 
UniProt
Find proteins for P94267 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth F]209Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth G]182Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth H]180Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth I]148Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10I [auth J]162Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11J [auth K]139Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth L]145Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14L [auth M]122Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15M [auth N]145Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16N [auth O]138Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17O [auth P]121Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18P [auth Q]119Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19Q [auth R]117Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth S]114Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth T]103Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth U]115Borreliella burgdorferi B31Mutation(s): 0 
UniProt
Find proteins for P94272 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth V]98Borreliella burgdorferi B31Mutation(s): 0 
UniProt
Find proteins for P94269 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth W]101Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth X]181Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth Y]74Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth Z]91Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth a]65Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein uL30AA [auth b]100Borreliella burgdorferi B31Mutation(s): 0 
UniProt
Find proteins for A0A0H3C073 (Borreliella burgdorferi (strain ZS7))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BBA [auth c]81Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth d]59Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth e]51Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth f]50Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth g]66Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth h]37Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein bL38HA [auth i]46Borreliella burgdorferi B31Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,929Borreliella burgdorferi B31
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA112Borreliella burgdorferi B31
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15
MODEL REFINEMENTPHENIX1.18

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM61576

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary