9I5T image
Deposition Date 2025-01-28
Release Date 2025-08-20
Last Version Date 2026-03-04
Entry Detail
PDB ID:
9I5T
Keywords:
Title:
50S subunit of P. gingivalis ribosome with Lefamulin
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:A (auth: 0)
Chain Length:79
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmC
Chain IDs:B (auth: 1)
Chain Length:64
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:C (auth: 11)
Chain Length:186
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE2
Chain IDs:D (auth: 12)
Chain Length:85
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplF
Chain IDs:DA (auth: 13)
Chain Length:183
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DUF4295 domain-containing pro
Gene (Uniprot):NY149_09915, NY151_00865
Chain IDs:CA (auth: 15)
Chain Length:49
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmD
Chain IDs:E (auth: 2)
Chain Length:58
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:F (auth: 4)
Chain Length:61
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:FA (auth: 5)
Chain Length:62
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:G (auth: 6)
Chain Length:50
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:H (auth: 7)
Chain Length:65
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmJ
Chain IDs:I (auth: 8)
Chain Length:38
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:J (auth: A)
Chain Length:2882
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:K (auth: B)
Chain Length:109
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:L (auth: D)
Chain Length:274
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:M (auth: E)
Chain Length:205
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:N (auth: F)
Chain Length:209
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:O (auth: M)
Chain Length:151
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplN
Chain IDs:EA (auth: N)
Chain Length:121
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:P (auth: O)
Chain Length:148
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:Q (auth: P)
Chain Length:144
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:R (auth: Q)
Chain Length:160
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:S (auth: R)
Chain Length:114
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:T (auth: S)
Chain Length:121
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:U (auth: T)
Chain Length:115
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:V (auth: U)
Chain Length:105
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:W (auth: V)
Chain Length:134
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:X (auth: W)
Chain Length:97
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:Y (auth: X)
Chain Length:106
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplY
Chain IDs:Z (auth: Y)
Chain Length:192
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:AA (auth: Z)
Chain Length:85
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:BA (auth: h)
Chain Length:179
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Primary Citation
Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Nucleic Acids Res. 53 ? ? (2025)
PMID: 40444637 DOI: 10.1093/nar/gkaf458

Abstact

Porphyromonas gingivalis, an anaerobic pathogen in chronic periodontitis, belongs to the Bacteroidota phylum and is associated with various virulence factors. Its antibiotic-resistant strains and its propensity to form biofilms pose a challenge to effective treatment. To explore therapeutic avenues, we studied the high-resolution cryogenic electron microscope structures of ribosomes from the wild-type P. gingivalis W83 and the macrolide-resistant mutant strain ermΔporN. The structural analysis revealed unique features primarily at the ribosome periphery. Together with the distinctive distribution of ribosomal RNA modifications, these findings offer insights into the therapeutical potential, such as creation of novel therapeutic compounds inhibiting the specific cellular functions of the P. gingivalis ribosomes. Moreover, the high-resolution structure of the ermΔporN ribosome in its complex with the approved antibiotic lefamulin suggests its repurposing against P. gingivalis. Furthermore, we provide a foundation for additional effective strategies to treat periodontitis and associated systemic diseases.

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