9I5X | pdb_00009i5x

Porphyromonas gingivalis 70S ribosome (W83 Strain)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.

Hiregange, D.G.Samiya, S.Mizgalska, D.Ben-Zeev, E.Waghalter, M.Rivalta, A.Rajan, K.S.Halfon, Y.Breiner-Goldstein, E.Kaczmarczyk, I.Sroka, A.Taoka, M.Nobe, Y.Isobe, T.Paukner, S.Zimmerman, E.Bashan, A.Potempa, J.Yonath, A.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf458
  • Primary Citation of Related Structures:  
    9I5T, 9I5V, 9I5X

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19A [auth p]89Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RLY8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28B [auth 0]79Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RM15 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29C [auth 1]64Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30D [auth 2]58Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32E [auth 4]61Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33F [auth 5]62Porphyromonas gingivalisMutation(s): 0 
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Find proteins for B2RM14 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34G [auth 6]50Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RIL8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35H [auth 7]65Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36I [auth 8]38Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2L [auth D]274Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3M [auth E]205Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4N [auth F]209Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10O [auth K]101Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11P [auth L]128Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13Q [auth M]151Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14R [auth N]121Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15S [auth O]148Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16T [auth P]144Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RLY5 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17U [auth Q]160Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18V [auth R]114Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19W [auth S]121Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RGQ9 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20X [auth T]115Porphyromonas gingivalisMutation(s): 0 
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Find proteins for Q7MVQ8 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21Y [auth U]105Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22Z [auth V]134Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23AA [auth W]97Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24BA [auth X]106Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27CA [auth Z]85Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6EA [auth b]117Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16FA [auth c]192Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20GA [auth d]84Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17HA [auth e]84Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15IA [auth f]89Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14JA [auth g]89Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9KA [auth h]179Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13LA [auth i]126Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12MA [auth j]134Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3NA [auth k]246Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4OA [auth l]201Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7PA [auth m]158Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTL0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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UniProt GroupQ7MTL0
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5QA [auth n]172Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTN0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25RA [auth Y]192Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RHF3 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8SA [auth o]131Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RLX8 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
AURKAIP1/COX24 domain-containing proteinTA [auth 10]30Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MV43 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9UA [auth J]128Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RL63 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18VA [auth I]90Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for B2RIG4 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S rRNAJ [auth A]2,889Porphyromonas gingivalis
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Entity ID: 11
MoleculeChains LengthOrganismImage
5S rRNAK [auth B]109Porphyromonas gingivalis
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Entity ID: 30
MoleculeChains LengthOrganismImage
16S rRNADA [auth a]1,534Porphyromonas gingivalis
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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XA [auth 4]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AB [auth A]
AC [auth A]
BB [auth A]
BC [auth A]
CB [auth A]
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CB [auth A],
CC [auth A],
DB [auth A],
EB [auth A],
EH [auth B],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
JB [auth A],
KB [auth A],
LB [auth A],
LH [auth W],
MB [auth A],
MH [auth X],
NB [auth A],
NH [auth a],
OB [auth A],
OH [auth a],
PB [auth A],
PH [auth a],
QB [auth A],
QH [auth a],
RB [auth A],
RH [auth a],
SB [auth A],
SH [auth a],
TB [auth A],
TH [auth a],
UB [auth A],
UH [auth a],
VB [auth A],
VH [auth a],
WB [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AH [auth A]
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth F],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth T],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth V],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth V],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
WA [auth 4],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth a],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth a],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth a],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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DC [auth A]
EC [auth A]
FC [auth A]
FH [auth B]
GC [auth A]
DC [auth A],
EC [auth A],
FC [auth A],
FH [auth B],
GC [auth A],
GH [auth B],
HC [auth A],
IC [auth A],
JC [auth A],
KC [auth A],
LC [auth A],
MC [auth A],
NC [auth A],
OC [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateIsraelTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release