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- PDB-9qt5: Structure of the 50S ribosomal subunit from the antibiotic-produc... -

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Basic information

Entry
Database: PDB / ID: 9qt5
TitleStructure of the 50S ribosomal subunit from the antibiotic-producing bacterium Streptomyces fradiae
Components
  • (Large ribosomal subunit protein ...) x 28
  • 23S rRNA
  • 5S rRNA
KeywordsRIBOSOME / Streptomyces / 50S / ribosome-targeting antibiotics
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / 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 / 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 L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. ...: / : / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9 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 L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L28/L24 superfamily / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / 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 L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal L32p protein family / Ribosomal protein L21 / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL14 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStreptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsEkemezie, C.L. / Melnikov, S.V.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N013840/1 United Kingdom
Royal SocietyRGS/R2/202003 United Kingdom
CitationJournal: Cell Rep / Year: 2025
Title: Extensive natural variation in bacterial ribosomal drug-binding sites.
Authors: Chinenye L Ekemezie / Lewis I Chan / Charlotte R Brown / Karla Helena-Bueno / Tom A Williams / Sergey V Melnikov /
Abstract: Ribosomes from certain bacteria possess divergent drug-binding sites compared to those of Escherichia coli, leading to natural evasion or hypersensitivity to antibiotics. However, in the absence of ...Ribosomes from certain bacteria possess divergent drug-binding sites compared to those of Escherichia coli, leading to natural evasion or hypersensitivity to antibiotics. However, in the absence of systematic studies, it is unknown whether this divergence is rare or common among bacterial species. Here, we address this by reconstructing the evolutionary history of drug-binding residues in bacterial ribosomes. We find that many rRNA residues that are currently viewed as bacterial-specific features of ribosomal drug-binding sites are in fact conserved only in a subset of bacteria. Conversely, species with divergent drug-binding sites are widespread in nature, arising from ancient rRNA polymorphisms at the direct ribosome-drug interface. Using a few bacterial species harboring divergent drug-binding sites, we identify their intrinsic resistance to corresponding ribosome-targeting antibiotics. Overall, we reveal the extensive lineage-specific diversity of ribosomal drug-binding sites, offering a resource for developing more targeted antibiotics and enabling personalized drug selection for specific pathogens.
History
DepositionApr 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Large ribosomal subunit protein uL16
2: 5S rRNA
B: Large ribosomal subunit protein uL2
C: Large ribosomal subunit protein uL3
D: Large ribosomal subunit protein uL4
E: Large ribosomal subunit protein uL5
F: Large ribosomal subunit protein uL6
G: Large ribosomal subunit protein bL9
J: Large ribosomal subunit protein uL13
K: Large ribosomal subunit protein uL14
O: Large ribosomal subunit protein uL18
L: Large ribosomal subunit protein uL15
P: Large ribosomal subunit protein bL19
Q: Large ribosomal subunit protein bL20
R: Large ribosomal subunit protein bL21
S: Large ribosomal subunit protein uL22
T: Large ribosomal subunit protein uL23
U: Large ribosomal subunit protein uL24
V: Large ribosomal subunit protein bL25
W: Large ribosomal subunit protein bL27
X: Large ribosomal subunit protein bL28
Y: Large ribosomal subunit protein uL29
Z: Large ribosomal subunit protein uL30
3: Large ribosomal subunit protein bL32
4: Large ribosomal subunit protein bL33
5: Large ribosomal subunit protein bL34
6: Large ribosomal subunit protein bL35
7: Large ribosomal subunit protein bL36
N: Large ribosomal subunit protein bL17
1: 23S rRNA


Theoretical massNumber of molelcules
Total (without water)1,431,85230
Polymers1,431,85230
Non-polymers00
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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Large ribosomal subunit protein ... , 28 types, 28 molecules MBCDEFGJKOLPQRSTUVWXYZ34567N

#1: Protein Large ribosomal subunit protein uL16


Mass: 15829.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NNE1
#3: Protein Large ribosomal subunit protein uL2


Mass: 30492.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM84
#4: Protein Large ribosomal subunit protein uL3


Mass: 22682.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM83
#5: Protein Large ribosomal subunit protein uL4


Mass: 23112.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM93
#6: Protein Large ribosomal subunit protein uL5


Mass: 20971.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM88
#7: Protein Large ribosomal subunit protein uL6


Mass: 19174.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NNJ7
#8: Protein Large ribosomal subunit protein bL9


Mass: 15794.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2P0X7
#9: Protein Large ribosomal subunit protein uL13


Mass: 16301.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NMA9
#10: Protein Large ribosomal subunit protein uL14


Mass: 13426.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM92
#11: Protein Large ribosomal subunit protein uL18


Mass: 13341.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NNX4
#12: Protein Large ribosomal subunit protein uL15


Mass: 16019.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NN24
#13: Protein Large ribosomal subunit protein bL19


Mass: 13173.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NTT8
#14: Protein Large ribosomal subunit protein bL20


Mass: 14460.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NZD1
#15: Protein Large ribosomal subunit protein bL21


Mass: 11600.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NZA8
#16: Protein Large ribosomal subunit protein uL22


Mass: 12846.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NNI7
#17: Protein Large ribosomal subunit protein uL23


Mass: 11849.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM78
#18: Protein Large ribosomal subunit protein uL24


Mass: 11709.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NM97
#19: Protein Large ribosomal subunit protein bL25 / General stress protein CTC


Mass: 20475.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2P3K7
#20: Protein Large ribosomal subunit protein bL27


Mass: 8844.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NZJ9
#21: Protein Large ribosomal subunit protein bL28


Mass: 6734.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NV37
#22: Protein Large ribosomal subunit protein uL29


Mass: 8417.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NMI9
#23: Protein Large ribosomal subunit protein uL30


Mass: 6932.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NMJ7
#24: Protein Large ribosomal subunit protein bL32


Mass: 6566.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NTQ5
#25: Protein Large ribosomal subunit protein bL33


Mass: 6423.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2P044
#26: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5313.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2P0X6
#27: Protein Large ribosomal subunit protein bL35


Mass: 7103.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NZ92
#28: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4403.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NMD2
#29: Protein Large ribosomal subunit protein bL17


Mass: 17701.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: UniProt: A0A1Y2NMK7

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RNA chain , 2 types, 2 molecules 21

#2: RNA chain 5S rRNA


Mass: 37883.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: GenBank: 1751465408
#30: RNA chain 23S rRNA


Mass: 1012266.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
References: GenBank: 1751465408

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Details

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: Streptomyces fradiae ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Streptomyces fradiae ATCC 10745 = DSM 40063 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethane-hydrochloricTris-HCl1
220 mMMagnesium acetateMgCH3C0021
350 mMPotassium ChlorideKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 77 K
Image recordingAverage exposure time: 7.94 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4219

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2cryoSPARC4.6image acquisition
4cryoSPARC4.6CTF correction
7UCSF ChimeraX1.9model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6final Euler assignment
12cryoSPARC4.6classification
13cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 966178
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250126 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE

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