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- PDB-9fco: Structure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex -

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Basic information

Entry
Database: PDB / ID: 9fco
TitleStructure of E. coli 30S-IF1-IF3-mRNA-Kasugamycin complex
Components
  • (Small ribosomal subunit protein ...) x 12
  • (Translation initiation factor IF- ...) x 2
  • 16S rRNA
  • mRNA
KeywordsTRANSLATION / Ribosome / Antibiotic
Function / homology
Function and homology information


ribosome disassembly / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / mRNA regulatory element binding translation repressor activity ...ribosome disassembly / ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / negative regulation of translational initiation / regulation of mRNA stability / translation initiation factor activity / mRNA regulatory element binding translation repressor activity / response to cold / positive regulation of RNA splicing / DNA endonuclease activity / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosome binding / ribosomal small subunit assembly / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain ...Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor IF-1 / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S11 / Ribosomal protein S12 signature. / RNA-binding S4 domain superfamily / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Chem-KSG / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Translation initiation factor IF-3 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 ...: / Chem-KSG / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Translation initiation factor IF-3 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein bS21 / Translation initiation factor IF-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSafdari, H.A. / Wilson, D.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: The translation inhibitors kasugamycin, edeine and GE81112 target distinct steps during 30S initiation complex formation.
Authors: Haaris A Safdari / Martino Morici / Ana Sanchez-Castro / Andrea Dallapè / Helge Paternoga / Anna Maria Giuliodori / Attilio Fabbretti / Pohl Milón / Daniel N Wilson /
Abstract: During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and ...During bacterial translation initiation, the 30S ribosomal subunit, initiation factors, and initiator tRNA define the reading frame of the mRNA. This process is inhibited by kasugamycin, edeine and GE81112, however, their mechanisms of action have not been fully elucidated. Here we present cryo-electron microscopy structures of 30S initiation intermediate complexes formed in the presence of kasugamycin, edeine and GE81112 at resolutions of 2.0-2.9 Å. The structures reveal that all three antibiotics bind within the E-site of the 30S and preclude 30S initiation complex formation. While kasugamycin and edeine affect early steps of 30S pre-initiation complex formation, GE81112 stalls pre-initiation complex formation at a further step by allowing start codon recognition, but impeding IF3 departure. Collectively, our work highlights how chemically distinct compounds binding at a conserved site on the 30S can interfere with translation initiation in a unique manner.
History
DepositionMay 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 16S rRNA
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, fully modified isoform
H: Small ribosomal subunit protein uS8
I: Translation initiation factor IF-1
J: Translation initiation factor IF-3
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
Y: mRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,64095
Polymers537,99516
Non-polymers2,64579
Water33,3101849
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 , 2 types, 2 molecules BY

#1: RNA chain 16S rRNA


Mass: 339708.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#16: RNA chain mRNA


Mass: 13074.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Small ribosomal subunit protein ... , 12 types, 12 molecules DEFHKLOPQRTU

#2: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8
#3: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#4: Protein Small ribosomal subunit protein bS6, fully modified isoform


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#5: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, b3306, JW3268 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W7
#8: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 15055.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK, b3297, JW3259 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7R9
#9: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13814.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3
#10: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, secC, b3165, JW3134 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#11: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP, b2609, JW2590 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T3
#12: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ, neaA, b3311, JW3273 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG63
#13: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR, b4202, JW4160 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7T7
#14: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT, b0023, JW0022 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7U7
#15: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU, b3065, JW3037 / Production host: Escherichia coli (E. coli) / References: UniProt: P68679

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Translation initiation factor IF- ... , 2 types, 2 molecules IJ

#6: Protein Translation initiation factor IF-1


Mass: 8262.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infA, b0884, JW0867 / Production host: Escherichia coli (E. coli) / References: UniProt: P69222
#7: Protein Translation initiation factor IF-3


Mass: 20600.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: infC, fit, srjA, b1718, JW5829 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A707

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Non-polymers , 4 types, 1928 molecules

#17: Chemical ChemComp-KSG / (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE / KASUGAMYCIN


Mass: 379.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O9 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#18: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 53 / Source method: obtained synthetically / Formula: Mg
#19: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: K
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1849 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Structure of E.coli 30S-IF1-IF3-mRNA-Kasugamycin complex
Type: RIBOSOME / Entity ID: #2-#7, #9-#16, #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 1100 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 1.14 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: REFMAC / Version: 5.8.0415 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332988 / Symmetry type: POINT

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