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- PDB-9i5x: Porphyromonas gingivalis 70S ribosome (W83 Strain) -

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Basic information

Entry
Database: PDB / ID: 9i5x
TitlePorphyromonas gingivalis 70S ribosome (W83 Strain)
Components
  • (Large ribosomal subunit protein ...) x 26
  • (Small ribosomal subunit protein ...) x 18
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • AURKAIP1/COX24 domain-containing protein
KeywordsRIBOSOME / Antibiotic / Lefamulin
Function / homology
Function and homology information


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 ...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 / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / : / Ribosomal protein L9, bacteria/chloroplast ...: / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / : / 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 L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / 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 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 S14/S29 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 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 L33 superfamily / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein L28/L24 / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / : / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L27 / Ribosomal protein S6 superfamily / Ribosomal L27 protein / Ribosomal protein S12, bacterial-type / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L21 / Ribosomal protein L19 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS20 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS20 / 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 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / 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 / 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: 3 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

Downloads & links

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Assembly

Deposited unit
p: Small ribosomal subunit protein uS19
0: Large ribosomal subunit protein bL28
1: Large ribosomal subunit protein uL29
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
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
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
Y: Large ribosomal subunit protein bL25
o: Small ribosomal subunit protein uS8
10: AURKAIP1/COX24 domain-containing protein
J: Small ribosomal subunit protein uS9
I: Small ribosomal subunit protein bS18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,092,793234
Polymers2,087,61348
Non-polymers5,180186
Water15,403855
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 ... , 18 types, 18 molecules pKLbcdefgijklmnoJI

#1: 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
#15: 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
#16: 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
#31: 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
#32: 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
#33: 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
#34: 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
#35: 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
#36: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#45: 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
#47: 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
#48: 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

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Large ribosomal subunit protein ... , 26 types, 26 molecules 01245678DEFMNOPQRSTUVWXZhY

#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#12: 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
#13: 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
#14: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#37: 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
#44: 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

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RNA chain , 3 types, 3 molecules ABa

#10: RNA chain 23S rRNA


Mass: 936413.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)
#11: RNA chain 5S rRNA


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


Mass: 496728.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)

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Protein/peptide , 1 types, 1 molecules 10

#46: 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 , 5 types, 1041 molecules

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


Mass: 24.305 Da / Num. of mol.: 128 / Source method: obtained synthetically / Formula: Mg
#50: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#51: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: K
#52: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#53: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: Porphyromonas gingivalis 70S ribosome (W83 Strain) / Type: RIBOSOME / Details: 70S ribosome of W83 strain
Entity ID: #2-#3, #46, #4-#14, #48, #47, #15-#28, #44, #29-#43, #45, #1
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (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: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129576 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004125677
ELECTRON MICROSCOPYf_angle_d0.659188389
ELECTRON MICROSCOPYf_dihedral_angle_d15.03550057
ELECTRON MICROSCOPYf_chiral_restr0.03824274
ELECTRON MICROSCOPYf_plane_restr0.0059831

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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