- EMDB-54782: Cryo-EM structure of the 70S ribosome from Francisella tularensis... -
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Basic information
Entry
Database: EMDB / ID: EMD-54782
Title
Cryo-EM structure of the 70S ribosome from Francisella tularensis bound to a hibernation-promoting factor
Map data
Sample
Complex: 70S Ribosome
RNA: x 3 types
Protein or peptide: x 50 types
Ligand: x 2 types
Keywords
Cryo-EM structure of the 70S ribosome from Francisella tularensis bound to a hibernation-promoting factor from HPF/YfiA family / RIBOSOME
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 / ribosomal small subunit assembly / transferase activity / 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 / ribosomal small subunit assembly / transferase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / 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 L16 signature 1. / Ribosomal protein L9 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / 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 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 L5, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S4, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S5, bacterial-type / 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 L33 / Ribosomal protein S18, conserved site / Ribosomal L28 family / Ribosomal protein S18 signature. / Ribosomal protein L33 superfamily / Ribosomal protein S9, bacterial/plastid / 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
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 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL24 ...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 / Large ribosomal subunit protein uL16 / 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 species
Francisella tularensis (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 2.39 Å
Ministry of Education, Youth and Sports of the Czech Republic
NIVB
Czech Republic
Citation
Journal: 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.
Name: MAGNESIUM ION / type: ligand / ID: 54 / Number of copies: 135 / Formula: MG
Molecular weight
Theoretical: 24.305 Da
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Macromolecule #55: ZINC ION
Macromolecule
Name: ZINC ION / type: ligand / ID: 55 / Number of copies: 1 / Formula: ZN
Molecular weight
Theoretical: 65.409 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.5 Component:
Concentration
Formula
Name
20.0 mM
HEPES
HEPES
20.0 mM
KCl
potasium chloride
20.0 mM
MgCl2
magnesium chloride
Grid
Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
TFS KRIOS
Image recording
Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 30000 / Average electron dose: 40.0 e/Å2 / Details: 24869 images were used for final map
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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