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- PDB-9xtd: E.coli delta lepA 30S ribosomal subunit class B, body domain -

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Basic information

Entry
Database: PDB / ID: 9xtd
TitleE.coli delta lepA 30S ribosomal subunit class B, body domain
Components
  • (Small ribosomal subunit protein ...) x 11
  • 30S ribosomal protein S16
  • RNA (1128-MER)
KeywordsRIBOSOME / 30S subunit maturation / LepA / cryo-EM / ribosome assembly
Function / homology
Function and homology information


ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription antitermination ...ornithine decarboxylase inhibitor activity / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / transcription antitermination / DNA endonuclease activity / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / regulation of translation / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / response to antibiotic / hydrolase activity / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / 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 / Ribosomal protein S5, bacterial-type ...Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / 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 / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / : / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / 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, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / S4 RNA-binding domain / Ribosomal S11, conserved site / S4 domain / Ribosomal protein S11 signature. / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / 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
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS18 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / 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 uS2 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsKravchenko, O.V. / Maksimova, E.M. / Baymukhametov, T.N. / Stolboushkina, E.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20186 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2026
Title: The Conserved GTPase LepA May Contribute to the Final Proper Stabilization of the 3' Domain of the 30S Subunit During Ribosome Assembly.
Authors: Olesya Kravchenko / Elena Maksimova / Timur Baymukhametov / Irina Eliseeva / Elena Stolboushkina /
Abstract: The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal ...The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an strain with a deleted gene. The cryo-EM maps for ∆ 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3' end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of Δ 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3' domain of the 30S subunit during ribosome assembly.
History
DepositionNov 22, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (1128-MER)
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6, non-modified isoform
H: Small ribosomal subunit protein uS8
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
O: Small ribosomal subunit protein uS15
P: 30S ribosomal protein S16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
T: Small ribosomal subunit protein bS20
B: Small ribosomal subunit protein uS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)662,79752
Polymers661,84913
Non-polymers94839
Water33,6701869
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Small ribosomal subunit protein ... , 11 types, 11 molecules DEFHKLOQRTB

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


Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V8
#3: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W3
#4: Protein Small ribosomal subunit protein bS6, non-modified isoform


Mass: 12326.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#5: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#6: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9
#7: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: D2T-(3R)-3-(methylsulfanyl)-L-aspartic acid post-translational modification in the protein
Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7S3
#8: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADZ4
#10: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AG63
#11: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 6466.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T7
#12: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7U7
#13: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 24971.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7V0

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RNA chain / Protein , 2 types, 2 molecules AP

#1: RNA chain RNA (1128-MER)


Mass: 499775.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Post-transcriptional modifications: PSU - PSEUDOURIDINE-5'-MONOPHOSPHATE; G7M - N7-METHYL-GUANOSINE-5'-MONOPHOSPHATE; 2MG - 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE; MA6 - 6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
Source: (natural) Escherichia coli (E. coli) / References: GenBank: 2970342069
#9: Protein 30S ribosomal protein S16 / Small ribosomal subunit protein bS16


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7T3

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Non-polymers , 2 types, 1908 molecules

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


Mass: 24.305 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1869 / 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: E.coli delta lepA 30S ribosomal subunit class B, body domain
Type: RIBOSOME / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 72 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
4Warp1.0.9CTF correction
13cryoSPARC4.6.13D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 269839 / Symmetry type: POINT

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