8FMW image
Deposition Date 2022-12-25
Release Date 2023-11-08
Last Version Date 2024-11-20
Entry Detail
PDB ID:
8FMW
Keywords:
Title:
The structure of a hibernating ribosome in the Lyme disease pathogen
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.86 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1529
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:X (auth: AA)
Chain Length:65
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Y (auth: AB)
Chain Length:100
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:Z (auth: AC)
Chain Length:81
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: AD)
Chain Length:59
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:BA (auth: AE)
Chain Length:206
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: AF)
Chain Length:209
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: AG)
Chain Length:66
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:EA (auth: AH)
Chain Length:37
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: AI)
Chain Length:46
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:GA (auth: AJ)
Chain Length:162
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:HA (auth: AK)
Chain Length:139
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:IA (auth: AL)
Chain Length:145
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:JA (auth: AM)
Chain Length:122
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:KA (auth: AN)
Chain Length:145
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:LA (auth: AO)
Chain Length:138
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:MA (auth: AP)
Chain Length:121
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:NA (auth: AQ)
Chain Length:119
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:OA (auth: AR)
Chain Length:117
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:PA (auth: AS)
Chain Length:114
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:QA (auth: AT)
Chain Length:103
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:RA (auth: AU)
Chain Length:115
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:SA (auth: AV)
Chain Length:98
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:TA (auth: AW)
Chain Length:101
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:UA (auth: AX)
Chain Length:181
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:VA (auth: AY)
Chain Length:74
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:WA (auth: AZ)
Chain Length:91
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:XA (auth: Aa)
Chain Length:65
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein uL30
Chain IDs:YA (auth: Ab)
Chain Length:100
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31 type B
Gene (Uniprot):rpmE2
Chain IDs:ZA (auth: Ac)
Chain Length:81
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AB (auth: Ad)
Chain Length:59
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BB (auth: Ae)
Chain Length:206
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CB (auth: Af)
Chain Length:209
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DB (auth: Ag)
Chain Length:66
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EB (auth: Ah)
Chain Length:37
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL38
Gene (Uniprot):BB_0162
Chain IDs:FB (auth: Ai)
Chain Length:46
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:B (auth: C)
Chain Length:206
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:C (auth: D)
Chain Length:208
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:D (auth: E)
Chain Length:158
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:E (auth: F)
Chain Length:97
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:F (auth: G)
Chain Length:157
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:G (auth: H)
Chain Length:132
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:H (auth: I)
Chain Length:131
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:I (auth: J)
Chain Length:102
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:J (auth: K)
Chain Length:117
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:K (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: M)
Chain Length:114
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:M (auth: N)
Chain Length:60
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:N (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: P)
Chain Length:83
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:P (auth: Q)
Chain Length:82
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: R)
Chain Length:63
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: S)
Chain Length:84
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: T)
Chain Length:85
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:T (auth: U)
Chain Length:69
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein bS22
Chain IDs:U (auth: V)
Chain Length:28
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal subunit interface protein
Gene (Uniprot):BB_0449
Chain IDs:V (auth: W)
Chain Length:97
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Polymer Type:polyribonucleotide
Molecule:E-site t-RNA
Chain IDs:W (auth: X)
Chain Length:76
Number of Molecules:1
Biological Source:Borreliella burgdorferi B31
Ligand Molecules
Primary Citation
The structure of a hibernating ribosome in a Lyme disease pathogen.
Nat Commun 14 6961 6961 (2023)
PMID: 37907464 DOI: 10.1038/s41467-023-42266-7

Abstact

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.

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Protein

Chemical

Disease

Primary Citation of related structures
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