9I5T | pdb_00009i5t

50S subunit of P. gingivalis ribosome with Lefamulin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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
Large ribosomal subunit protein bL28A [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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29B [auth 1]64Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5C [auth 11]186Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BD [auth 12]85Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30E [auth 2]58Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32F [auth 4]61Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34G [auth 6]50Porphyromonas gingivalisMutation(s): 0 
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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 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2L [auth D]274Porphyromonas gingivalisMutation(s): 0 
UniProt
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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
Large ribosomal subunit protein uL13O [auth M]151Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15P [auth O]148Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16Q [auth P]144Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17R [auth Q]160Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18S [auth R]114Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19T [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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20U [auth T]115Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21V [auth U]105Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22W [auth V]134Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23X [auth W]97Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for A0A134DR82 (Porphyromonas gingivalis)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24Y [auth X]106Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25Z [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: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27AA [auth Z]85Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9BA [auth h]179Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4295 domain-containing proteinCA [auth 15]49Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6DA [auth 13]183Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14EA [auth N]121Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33FA [auth 5]62Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 10
MoleculeChains LengthOrganismImage
23S rRNAJ [auth A]2,882Porphyromonas gingivalis
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Entity ID: 11
MoleculeChains LengthOrganismImage
5S rRNAK [auth B]109Porphyromonas gingivalis
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
62B
Query on 62B

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IA [auth A]Lefamulin
C28 H45 N O5 S
KPVIXBKIJXZQJX-FCEONZPQSA-N
ZN
Query on ZN

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

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AG [auth A]
BG [auth A]
CG [auth A]
DG [auth A]
EG [auth A]
AG [auth A],
BG [auth A],
CG [auth A],
DG [auth A],
EG [auth A],
NF [auth A],
OF [auth A],
PF [auth A],
QF [auth A],
RF [auth A],
SF [auth A],
TF [auth A],
UF [auth A],
VF [auth A],
WF [auth A],
XF [auth A],
YF [auth A],
ZF [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GA [auth 4],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SG [auth B],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VG [auth F],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WG [auth V],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XG [auth V],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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FG [auth A]
GG [auth A]
HG [auth A]
IG [auth A]
JG [auth A]
FG [auth A],
GG [auth A],
HG [auth A],
IG [auth A],
JG [auth A],
KG [auth A],
LG [auth A],
MG [auth A],
NG [auth A],
OG [auth A],
PG [auth A],
QG [auth A],
RG [auth A],
TG [auth B],
UG [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateTHE 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