9I5V | pdb_00009i5v

70S P. gingivalis ribosome erm-delta-porN strain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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 bS18A [auth I]90Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29B [auth 1]64Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28C [auth 0]79Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5D [auth 11]186Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31BE [auth 12]85Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6F [auth 13]183Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-associated translation inhibitor RaiAG [auth 14]401Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30H [auth 2]58Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32I [auth 4]61Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33J [auth 5]62Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34K [auth 6]50Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35L [auth 7]65Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36M [auth 8]38Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21N [auth 9]63Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2Q [auth D]274Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3R [auth E]205Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4S [auth F]209Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10T [auth K]101Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11U [auth L]128Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13V [auth M]151Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14W [auth N]121Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15X [auth O]148Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16Y [auth P]144Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17Z [auth Q]160Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18AA [auth R]114Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19BA [auth S]121Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20CA [auth T]115Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21DA [auth U]105Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22EA [auth V]134Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23FA [auth W]97Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24GA [auth X]106Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25HA [auth Y]192Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27IA [auth Z]85Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6KA [auth b]117Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16LA [auth c]192Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20MA [auth d]84Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17NA [auth e]84Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15OA [auth f]89Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14PA [auth g]89Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9QA [auth h]179Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13RA [auth i]126Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12SA [auth j]134Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTK9 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3TA [auth k]246Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTL9 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4UA [auth l]201Porphyromonas gingivalisMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7VA [auth m]158Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTL0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5WA [auth n]172Porphyromonas gingivalisMutation(s): 0 
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Find proteins for Q7MTN0 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8XA [auth o]131Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MTM7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4295 domain-containing proteinYA [auth 15]49Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for A0A0E2LR73 (Porphyromonas gingivalis F0570)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
AURKAIP1/COX24 domain-containing proteinZA [auth 10]30Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MV43 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19AB [auth p]89Porphyromonas gingivalisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9BB [auth J]128Porphyromonas gingivalisMutation(s): 0 
UniProt
Find proteins for Q7MX42 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
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Entity ID: 15
MoleculeChains LengthOrganismImage
23S rRNAO [auth A]2,889Porphyromonas gingivalis
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Entity ID: 16
MoleculeChains LengthOrganismImage
5S rRNAP [auth B]109Porphyromonas gingivalis
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Entity ID: 36
MoleculeChains LengthOrganismImage
16S rRNAJA [auth a]1,534Porphyromonas gingivalis
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
AC [auth A]
BC [auth A]
BH [auth B]
DB [auth A]
EB [auth A]
AC [auth A],
BC [auth A],
BH [auth B],
DB [auth A],
EB [auth A],
FB [auth A],
GB [auth A],
HB [auth A],
IB [auth A],
IH [auth a],
JB [auth A],
JH [auth a],
KB [auth A],
KH [auth a],
LB [auth A],
LH [auth a],
MB [auth A],
MH [auth a],
NB [auth A],
OB [auth A],
PB [auth A],
QB [auth A],
RB [auth A],
SB [auth A],
TB [auth A],
UB [auth A],
VB [auth A],
WB [auth A],
XB [auth A],
YB [auth A],
ZB [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
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],
CB [auth 4],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth B],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth F],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth V],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth V],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
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],
OH [auth a],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth a],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth a],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth a],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth a],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth a],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth a],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth a],
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 10],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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CC [auth A]
CH [auth B]
DC [auth A]
DH [auth B]
EC [auth A]
CC [auth A],
CH [auth B],
DC [auth A],
DH [auth B],
EC [auth A],
FC [auth A],
GC [auth A],
HC [auth A],
IC [auth A],
JC [auth A],
KC [auth A],
LC [auth A],
MC [auth A],
NC [auth A],
NH [auth a],
OC [auth A],
PC [auth A],
QC [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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