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- PDB-28ye: 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteoba... -

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Basic information

Entry
Database: PDB / ID: 28ye
Title50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
Components
  • (Large ribosomal subunit protein ...) x 26
  • 23S rRNA
  • 5S rRNA (fragment)
  • E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)
  • Ribosome silencing factor S
KeywordsRIBOSOME / 50S / RsfS
Function / homology: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesAsaia platycodi JCM 25414 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsChan, L.I. / Omae, K. / Amikura, K. / Suzuki, S. / Melnikov, S.M.
Funding support United Kingdom, Japan, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008695/1 United Kingdom
Royal SocietyICA/R2/242249 United Kingdom
Japan Science and TechnologyJPMJCR20S4 Japan
CitationJournal: BioRXiv / Year: 2025
Title: The Evolutionary Lifecycle of Ribosome Hibernation Factors
Authors: Chan, L.I. / Melnikov, S.V.
History
DepositionFeb 27, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data 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
Z: Large ribosomal subunit protein bL36
A: Large ribosomal subunit protein uL2
B: 23S rRNA
C: Large ribosomal subunit protein bL35
D: Large ribosomal subunit protein bL34
E: Large ribosomal subunit protein bL33
F: Large ribosomal subunit protein bL32
H: Large ribosomal subunit protein uL30
I: Large ribosomal subunit protein uL29
J: Large ribosomal subunit protein bL28
K: Large ribosomal subunit protein bL27
L: Large ribosomal subunit protein bL25
M: Large ribosomal subunit protein uL24
N: Large ribosomal subunit protein uL23
O: Large ribosomal subunit protein uL22
P: Large ribosomal subunit protein bL21
Q: Large ribosomal subunit protein bL20
S: Large ribosomal subunit protein bL17
T: Large ribosomal subunit protein uL16
U: Large ribosomal subunit protein uL15
V: Large ribosomal subunit protein uL14
W: Large ribosomal subunit protein uL13
X: Large ribosomal subunit protein bL9
Y: Large ribosomal subunit protein uL6
a: Large ribosomal subunit protein uL4
b: Large ribosomal subunit protein uL3
c: E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)
d: 5S rRNA (fragment)
R: Large ribosomal subunit protein bL19
G: Ribosome silencing factor S


Theoretical massNumber of molelcules
Total (without water)1,307,08230
Polymers1,307,08230
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 ... , 26 types, 26 molecules ZACDEFHIJKLMNOPQSTUVWXYabR

#1: Protein/peptide Large ribosomal subunit protein bL36


Mass: 4943.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#2: Protein Large ribosomal subunit protein uL2


Mass: 30385.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#4: Protein Large ribosomal subunit protein bL35


Mass: 7580.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#5: Protein/peptide Large ribosomal subunit protein bL34


Mass: 5270.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#6: Protein Large ribosomal subunit protein bL33


Mass: 6330.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#7: Protein Large ribosomal subunit protein bL32


Mass: 7436.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#8: Protein Large ribosomal subunit protein uL30


Mass: 6549.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#9: Protein Large ribosomal subunit protein uL29


Mass: 8423.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#10: Protein Large ribosomal subunit protein bL28


Mass: 11121.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#11: Protein Large ribosomal subunit protein bL27


Mass: 9183.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#12: Protein Large ribosomal subunit protein bL25


Mass: 22683.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#13: Protein Large ribosomal subunit protein uL24


Mass: 11483.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#14: Protein Large ribosomal subunit protein uL23


Mass: 12480.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#15: Protein Large ribosomal subunit protein uL22


Mass: 15759.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#16: Protein Large ribosomal subunit protein bL21


Mass: 11301.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#17: Protein Large ribosomal subunit protein bL20


Mass: 14604.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#18: Protein Large ribosomal subunit protein bL17


Mass: 15573.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#19: Protein Large ribosomal subunit protein uL16


Mass: 15212.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#20: Protein Large ribosomal subunit protein uL15


Mass: 16795.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#21: Protein Large ribosomal subunit protein uL14


Mass: 13324.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#22: Protein Large ribosomal subunit protein uL13


Mass: 17559.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#23: Protein Large ribosomal subunit protein bL9


Mass: 21119.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#24: Protein Large ribosomal subunit protein uL6


Mass: 19490.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#25: Protein Large ribosomal subunit protein uL4


Mass: 21742.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#26: Protein Large ribosomal subunit protein uL3


Mass: 24438.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#29: Protein Large ribosomal subunit protein bL19


Mass: 14342.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Modelled from the close relative Asaia bogorensis / Source: (natural) Asaia platycodi JCM 25414 (bacteria)

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RNA chain , 3 types, 3 molecules Bcd

#3: RNA chain 23S rRNA


Mass: 883724.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria) / References: GenBank: 3054411333
#27: RNA chain E-site tRNA (heterogeneous fragment modelled as poly-U with the CCA-end)


Mass: 5487.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)
#28: RNA chain 5S rRNA (fragment)


Mass: 36341.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria) / References: GenBank: 3054411333

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Protein , 1 types, 1 molecules G

#30: Protein Ribosome silencing factor S


Mass: 16392.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Asaia platycodi JCM 25414 (bacteria)

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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: Structure of the 50S ribosomal subunit with E-tRNA and RsfS from the alphaproteobacteria Asaia platycodi
Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Asaia platycodi JCM 25414 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris hydrochlorideTris-HCl1
220 mMMagnesium acetateMg(CH3COO)21
350 KClPotassium chlorideKCl1
SpecimenConc.: 0.642 mg/ml / Embedding 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 K

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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: 300 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC5.0.0particle selectioncryoSPARC was used to process cryo-EM data
4cryoSPARC5.0.0CTF correctioncryoSPARC was used to process cryo-EM data
13cryoSPARC5.0.03D reconstructioncryoSPARC was used to process cryo-EM data
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48969 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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