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- PDB-9t6h: Cryo-EM structure of the 70S ribosome from Francisella tularensis... -

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Basic information

Entry
Database: PDB / ID: 9t6h
TitleCryo-EM structure of the 70S ribosome from Francisella tularensis bound to antibiotics chloramphenicol and gentamicin
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 20
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / Ribosome-associated inhibitor A RaiA Chloramphenicol Gentamicin
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosomal small subunit assembly / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / 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 / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A ...: / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / 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 L9 signature. / Ribosomal protein L16 signature 1. / 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 L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L28/L24 superfamily / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein L6, bacterial-type / 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 / Ribosomal protein S5, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16
Similarity search - Domain/homology
CHLORAMPHENICOL / Chem-LLL / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS9 ...CHLORAMPHENICOL / Chem-LLL / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS9 / Ribosome hibernation promoting factor / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein bS21B / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSilhan, J. / Klima, M. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation Czech Republic
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure of the hibernating Francisella tularensis ribosome and mechanistic insights into its inhibition by antibiotics.
Authors: Martin Klima / Jan Silhan / Pavla Pavlik / Kamil Hercik / Evzen Boura /
Abstract: Francisella tularensis is the causative agent of tularemia, a zoonotic disease named after the Tulare County, California. Symptoms include sudden fever, chills, fatigue, and swollen lymph nodes, ...Francisella tularensis is the causative agent of tularemia, a zoonotic disease named after the Tulare County, California. Symptoms include sudden fever, chills, fatigue, and swollen lymph nodes, among others, and without treatment it is very serious or even fatal. In addition, F. tularensis is considered a potential bioterrorism threat due to its high infectivity and lethality. Ribosomes are key targets for many classes of antibiotics. In this study, we examined the F. tularensis ribosome and determined its structure at 2.5Å resolution using cryo-electron microscopy. Notably, we observed the stress-induced ribosome-associated inhibitor A (RaiA) protein bound to the ribosome. RaiA functions as a molecular hibernation factor, inhibiting bacterial translation in response to stress or nutrient deprivation. This mechanism parallels that described in the model organism Escherichia coli and in several pathogenic bacteria, such as Staphylococcus aureus. Furthermore, we solved structures of the antibiotics chloramphenicol and gentamicin bound to the F. tularensis ribosome. Collectively, these results provide structural insights that highlight previously unexplored opportunities for therapeutic intervention.
History
DepositionNov 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 23S ribosomal RNA
B: 5S ribosomal RNA
C: Large ribosomal subunit protein uL2
D: Large ribosomal subunit protein uL3
E: Large ribosomal subunit protein uL4
F: Large ribosomal subunit protein uL5
G: Large ribosomal subunit protein uL6
H: Large ribosomal subunit protein bL9
I: Large ribosomal subunit protein uL13
J: Large ribosomal subunit protein uL14
K: Large ribosomal subunit protein uL15
L: Large ribosomal subunit protein uL16
M: Large ribosomal subunit protein bL17
N: Large ribosomal subunit protein uL18
O: Large ribosomal subunit protein bL19
P: Large ribosomal subunit protein bL20
Q: Large ribosomal subunit protein bL21
R: Large ribosomal subunit protein uL22
S: Large ribosomal subunit protein uL23
T: Large ribosomal subunit protein uL24
U: Large ribosomal subunit protein bL25
V: Large ribosomal subunit protein bL27
W: Large ribosomal subunit protein bL28
X: Large ribosomal subunit protein uL29
Y: Large ribosomal subunit protein uL30
Z: Large ribosomal subunit protein bL31
0: Large ribosomal subunit protein bL32
1: Large ribosomal subunit protein bL33
2: Large ribosomal subunit protein bL34
3: Large ribosomal subunit protein bL35
4: Large ribosomal subunit protein bL36
a: 16S ribosomal RNA
b: Small ribosomal subunit protein uS2
c: Small ribosomal subunit protein uS3
d: Small ribosomal subunit protein uS4
e: Small ribosomal subunit protein uS5
f: Small ribosomal subunit protein bS6
g: Small ribosomal subunit protein uS7
h: Small ribosomal subunit protein uS8
i: Small ribosomal subunit protein uS9
j: Small ribosomal subunit protein uS10
k: Small ribosomal subunit protein uS11
l: Small ribosomal subunit protein uS12
m: Small ribosomal subunit protein uS13
n: Small ribosomal subunit protein uS14
o: Small ribosomal subunit protein uS15
p: Small ribosomal subunit protein bS16
q: Small ribosomal subunit protein uS17
r: Small ribosomal subunit protein bS18
s: Small ribosomal subunit protein uS19
t: Small ribosomal subunit protein bS20
u: Small ribosomal subunit protein bS21B
9: Ribosome hibernation promoting factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,142,067200
Polymers2,134,32753
Non-polymers7,740147
Water00
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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RNA chain , 3 types, 3 molecules ABa

#1: RNA chain 23S ribosomal RNA


Mass: 935337.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: GenBank: 1953470990
#2: RNA chain 5S ribosomal RNA


Mass: 36996.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria)
#32: RNA chain 16S ribosomal RNA


Mass: 495164.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: GenBank: 1919226889

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Large ribosomal subunit protein ... , 29 types, 29 molecules CDEFGHIJKLMNOPQRSTUVWXYZ01234

#3: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30469.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9S9
#4: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 22339.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JC0
#5: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22587.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JB9
#6: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20028.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9T7
#7: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19106.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9U0
#8: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 16107.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NC56
#9: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 15969.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q2A332
#10: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13259.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JB0
#11: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15126.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9U4
#12: Protein Large ribosomal subunit protein uL16


Mass: 15742.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A0A0B3VDL9
#13: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 16818.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9V0
#14: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13064.138 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JA4
#15: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13334.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NEB0
#16: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13378.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NDB3
#17: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 11585.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NDG2
#18: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12223.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JB5
#19: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 11156.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9S8
#20: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11498.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9T6
#21: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25


Mass: 10925.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NBX3
#22: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 9055.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NDG1
#23: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 8960.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14G26
#24: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7819.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q2A5G2
#25: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 6884.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JA2
#26: Protein Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 8284.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q2A2S8
#27: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6895.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NCH9
#28: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 6158.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14G25
#29: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5198.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JK5
#30: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7390.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14I18
#31: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4437.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14J99

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Small ribosomal subunit protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu

#33: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 24729.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9R4
#34: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 23338.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JB4
#35: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23148.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14J96
#36: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17554.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q2A5F3
#37: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 13075.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14HF1
#38: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17844.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JC3
#39: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14431.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9T9
#40: Protein Small ribosomal subunit protein uS9


Mass: 14764.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A0A0E2ZLL8
#41: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11917.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9S5
#42: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13786.841 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9U7
#43: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13846.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JC4
#44: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13406.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14J98
#45: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14


Mass: 11742.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JA7
#46: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10383.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NDP4
#47: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9091.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NEB3
#48: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9874.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9T4
#49: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 8395.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7NC55
#50: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10523.450 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q14JB6
#51: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 10173.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A7N9A3
#52: Protein Small ribosomal subunit protein bS21B / 30S ribosomal protein S21 2


Mass: 7863.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: Q2A3F5

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Protein , 1 types, 1 molecules 9

#53: Protein Ribosome hibernation promoting factor / Hibernation factor HPF


Mass: 11129.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Francisella tularensis (bacteria) / References: UniProt: A0A4E0P7K7

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Non-polymers , 4 types, 147 molecules

#54: Chemical
ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C19H39N5O7 / Feature type: SUBJECT OF INVESTIGATION
#55: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 136 / Source method: obtained synthetically / Formula: Mg
#56: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#57: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
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 Ribosome from Francisella tularensis, combined with antibiotics
Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Francisella (bacteria)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES 7.5
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 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: 3600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 9SDR

9sdr
PDB Unreleased entry


Accession code: 9SDR / Source name: PDB / Type: experimental model

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