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- PDB-9i5v: 70S P. gingivalis ribosome erm-delta-porN strain -

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Basic information

Entry
Database: PDB / ID: 9i5v
Title70S P. gingivalis ribosome erm-delta-porN strain
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 19
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • AURKAIP1/COX24 domain-containing protein
  • DUF4295 domain-containing protein
  • Ribosome-associated translation inhibitor RaiA
KeywordsRIBOSOME / macrolide-resistant
Function / homology
Function and homology information


chromosome segregation / DNA integration / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...chromosome segregation / DNA integration / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / DNA recombination / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / mRNA binding / DNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain ...Protein of unknown function DUF4295 / Domain of unknown function (DUF4295) / : / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / DNA breaking-rejoining enzyme, catalytic core / Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein S13, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S14/S29 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Ribosome-associated translation inhibitor RaiA / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Ribosome-associated translation inhibitor RaiA / DUF4295 domain-containing protein / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL31B / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL17 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL15 / AURKAIP1/COX24 domain-containing protein / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL21
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHiregange, D.G. / Bashan, A. / Yonath, A.
Funding support Israel, 1items
OrganizationGrant numberCountry
Other privateTHE HELEN AND MILTON A. KIMMELMAN CENTER FOR BIOMOLECULAR STRUCTURE AND ASSEMBLY Israel
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural studies of ribosome from an anaerobic Bacteroidetes human pathogen Porphyromonas gingivalis.
Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor ...Authors: Disha-Gajanan Hiregange / Sarit Samiya / Danuta Mizgalska / Efrat Ben-Zeev / Miriam Waghalter / Andre Rivalta / K Shanmugha Rajan / Yehuda Halfon / Elinor Breiner-Goldstein / Igor Kaczmarczyk / Aneta Sroka / Masato Taoka / Yuko Nobe / Toshiaki Isobe / Susanne Paukner / Ella Zimmerman / Anat Bashan / Jan Potempa / Ada Yonath /
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 ...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.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Small ribosomal subunit protein bS18
1: Large ribosomal subunit protein uL29
0: Large ribosomal subunit protein bL28
11: Large ribosomal subunit protein uL5
12: Large ribosomal subunit protein bL31B
13: Large ribosomal subunit protein uL6
14: Ribosome-associated translation inhibitor RaiA
2: Large ribosomal subunit protein uL30
4: Large ribosomal subunit protein bL32
5: Large ribosomal subunit protein bL33
6: Large ribosomal subunit protein bL34
7: Large ribosomal subunit protein bL35
8: Large ribosomal subunit protein bL36
9: Small ribosomal subunit protein bS21
A: 23S rRNA
B: 5S rRNA
D: Large ribosomal subunit protein uL2
E: Large ribosomal subunit protein uL3
F: Large ribosomal subunit protein uL4
K: Small ribosomal subunit protein uS10
L: Small ribosomal subunit protein uS11
M: Large ribosomal subunit protein uL13
N: Large ribosomal subunit protein uL14
O: Large ribosomal subunit protein uL15
P: Large ribosomal subunit protein uL16
Q: Large ribosomal subunit protein bL17
R: Large ribosomal subunit protein uL18
S: Large ribosomal subunit protein bL19
T: Large ribosomal subunit protein bL20
U: Large ribosomal subunit protein bL21
V: Large ribosomal subunit protein uL22
W: Large ribosomal subunit protein uL23
X: Large ribosomal subunit protein uL24
Y: Large ribosomal subunit protein bL25
Z: Large ribosomal subunit protein bL27
a: 16S rRNA
b: Small ribosomal subunit protein bS6
c: Small ribosomal subunit protein bS16
d: Small ribosomal subunit protein bS20
e: Small ribosomal subunit protein uS17
f: Small ribosomal subunit protein uS15
g: Small ribosomal subunit protein uS14
h: Large ribosomal subunit protein bL9
i: Small ribosomal subunit protein uS13
j: Small ribosomal subunit protein uS12
k: Small ribosomal subunit protein uS3
l: Small ribosomal subunit protein uS4
m: Small ribosomal subunit protein uS7
n: Small ribosomal subunit protein uS5
o: Small ribosomal subunit protein uS8
15: DUF4295 domain-containing protein
10: AURKAIP1/COX24 domain-containing protein
p: Small ribosomal subunit protein uS19
J: Small ribosomal subunit protein uS9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,203,000232
Polymers2,198,23954
Non-polymers4,761178
Water18,1051005
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Small ribosomal subunit protein ... , 19 types, 19 molecules I9KLbcdefgijklmnopJ

#1: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 10644.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG4
#14: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 7432.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MX34
#20: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11468.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLZ3
#21: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13857.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW7
#37: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 13613.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG3
#38: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 20703.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MT66
#39: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9711.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RHR8
#40: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10020.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY3
#41: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10584.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLH2
#42: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 9970.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX9
#44: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 14023.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW8
#45: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 14802.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTK9
#46: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 27620.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY6
#47: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 22969.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW6
#48: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 18134.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTL0
#49: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17870.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTN0
#50: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14823.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX8
#53: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 9929.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY8
#54: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 14556.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RL63

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Large ribosomal subunit protein ... , 29 types, 29 molecules 10111213245678DEFMNOPQRSTUVWXYZh

#2: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7499.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY4
#3: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9027.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RM15
#4: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20912.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY0
#5: Protein Large ribosomal subunit protein bL31B / 50S ribosomal protein L31 type B


Mass: 9816.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG0
#6: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 20389.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX7
#8: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6700.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLX4
#9: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6958.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RH62
#10: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 7356.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RM14
#11: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5761.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIL8
#12: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7518.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RJD8
#13: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4601.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW9
#17: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 29778.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY9
#18: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 21925.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLZ2
#19: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 23247.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTL4
#22: Protein Large ribosomal subunit protein uL13


Mass: 17075.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MX43
#23: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13086.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY2
#24: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15616.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTN2
#25: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 16344.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY5
#26: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 18074.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLW4
#27: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 12560.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MTM9
#28: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 14120.454 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RGQ9
#29: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13324.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MVQ8
#30: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11843.913 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MX95
#31: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 15357.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY7
#32: Protein Large ribosomal subunit protein uL23


Mass: 11116.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: A0A134DR82
#33: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11627.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLY1
#34: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 21028.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RHF3
#35: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9244.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RLC1
#43: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 19356.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: B2RIG5

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Protein , 1 types, 1 molecules 14

#7: Protein Ribosome-associated translation inhibitor RaiA


Mass: 46441.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: A0AAE9X5J6

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RNA chain , 3 types, 3 molecules ABa

#15: RNA chain 23S rRNA


Mass: 936466.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)
#16: RNA chain 5S rRNA


Mass: 35186.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)
#36: RNA chain 16S rRNA


Mass: 496748.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)

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Protein/peptide , 2 types, 2 molecules 1510

#51: Protein/peptide DUF4295 domain-containing protein


Mass: 5559.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: A0AAE9XCN0
#52: Protein/peptide AURKAIP1/COX24 domain-containing protein


Mass: 3827.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria) / References: UniProt: Q7MV43

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Non-polymers , 4 types, 1183 molecules

#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 129 / Source method: obtained synthetically / Formula: Mg
#56: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: K
#57: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1005 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 70S P. gingivalis ribosome erm-delta-porN strain / Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487:model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155090 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006131113
ELECTRON MICROSCOPYf_angle_d0.676196032
ELECTRON MICROSCOPYf_dihedral_angle_d14.59151324
ELECTRON MICROSCOPYf_chiral_restr0.04125212
ELECTRON MICROSCOPYf_plane_restr0.00510643

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