9I5X image
Deposition Date 2025-01-28
Release Date 2025-08-20
Last Version Date 2025-08-20
Entry Detail
PDB ID:
9I5X
Keywords:
Title:
Porphyromonas gingivalis 70S ribosome (W83 Strain)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.00 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 protein bL28
Gene (Uniprot):rpmB
Chain IDs:B (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 protein uL29
Gene (Uniprot):rpmC
Chain IDs:C (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:AURKAIP1/COX24 domain-containing protein
Gene (Uniprot):PG_1257
Chain IDs:TA (auth: 10)
Chain Length:30
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:D (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 protein bL32
Gene (Uniprot):rpmF
Chain IDs:E (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 protein bL33
Gene (Uniprot):rpmG
Chain IDs:F (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 protein bL34
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 protein bL35
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 protein bL36
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:1534
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:K (auth: B)
Chain Length:117
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
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 protein uL3
Gene (Uniprot):rplC
Chain IDs:M (auth: E)
Chain Length:84
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
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:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: I)
Chain Length:126
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:UA (auth: J)
Chain Length:134
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:O (auth: K)
Chain Length:246
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:P (auth: L)
Chain Length:128
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:Q (auth: M)
Chain Length:158
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:R (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 protein uL15
Gene (Uniprot):rplO
Chain IDs:S (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 protein uL16
Gene (Uniprot):rplP
Chain IDs:T (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 protein bL17
Gene (Uniprot):rplQ
Chain IDs:U (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 protein uL18
Gene (Uniprot):rplR
Chain IDs:V (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 protein bL19
Gene (Uniprot):rplS
Chain IDs:W (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 protein bL20
Gene (Uniprot):rplT
Chain IDs:X (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 protein bL21
Gene (Uniprot):rplU
Chain IDs:Y (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 protein uL22
Gene (Uniprot):rplV
Chain IDs:Z (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 protein uL23
Gene (Uniprot):rplW
Chain IDs:AA (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 protein uL24
Gene (Uniprot):rplX
Chain IDs:BA (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 protein bL25
Gene (Uniprot):rplY
Chain IDs:RA (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 protein bL27
Gene (Uniprot):rpmA
Chain IDs:CA (auth: Z)
Chain Length:85
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:DA (auth: a)
Chain Length:1534
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6
Gene (Uniprot):rpsF
Chain IDs:EA (auth: b)
Chain Length:117
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:FA (auth: c)
Chain Length:192
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:GA (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:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:HA (auth: e)
Chain Length:84
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:IA (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:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:JA (auth: g)
Chain Length:89
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:KA (auth: h)
Chain Length:179
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:LA (auth: i)
Chain Length:126
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:MA (auth: j)
Chain Length:134
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:NA (auth: k)
Chain Length:246
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:OA (auth: l)
Chain Length:128
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:PA (auth: m)
Chain Length:158
Number of Molecules:1
Biological Source:Porphyromonas gingivalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:QA (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:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:SA (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:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:A (auth: p)
Chain Length:144
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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Primary Citation of related structures
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