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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 L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / 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 L32p protein family / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / 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: To Be Published
Title: Evolution of drug-binding sites in bacterial ribosomes
Authors: Ekemezie, C.L. / Chan, L.I. / Brown, C.R. / Helena-Bueno, K. / Williams, T.A. / Melnikov, S.V.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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