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- PDB-8p6p: Mycoplasma pneumoniae small ribosomal subunit in chloramphenicol-... -

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Basic information

Entry
Database: PDB / ID: 8p6p
TitleMycoplasma pneumoniae small ribosomal subunit in chloramphenicol-treated cells
Components
  • (30S ribosomal protein ...) x 20
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 50S ribosomal protein L31
  • mRNA
  • tRNA-Asp (P-site)
  • tRNA-Lys (A-site)
KeywordsTRANSLATION / In situ / Ribosome / Chloramphenicol / cryo-ET
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type ...Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / 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 S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S2 signature 2. / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S5, C-terminal / Ribosomal protein S13 family profile. / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S13-like, H2TH
Similarity search - Domain/homology
PENTANE-1,5-DIAMINE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 ...PENTANE-1,5-DIAMINE / 1,4-DIAMINOBUTANE / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.2 Å
AuthorsSchacherl, M. / Xue, L. / Spahn, C.M.T. / Mahamid, J.
Funding support United States, Germany, 2items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeVisual Proteomics Imaging United States
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells.
Authors: Liang Xue / Christian M T Spahn / Magdalena Schacherl / Julia Mahamid /
Abstract: Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence ...Ribosome-targeting antibiotics represent an important class of antimicrobial drugs. Chloramphenicol (Cm) is a well-studied ribosomal peptidyl transferase center (PTC) binder and growing evidence suggests that its inhibitory action depends on the sequence of the nascent peptide. How such selective inhibition on the molecular scale manifests on the cellular level remains unclear. Here, we use cryo-electron tomography to analyze the impact of Cm inside the bacterium Mycoplasma pneumoniae. By resolving the Cm-bound ribosomes to 3.0 Å, we elucidate Cm's coordination with natural nascent peptides and transfer RNAs in the PTC. We find that Cm leads to the accumulation of a number of translation elongation states, indicating ongoing futile accommodation cycles, and to extensive ribosome collisions. We, thus, suggest that, beyond its direct inhibition of protein synthesis, the action of Cm may involve the activation of cellular stress responses. This work exemplifies how in-cell structural biology can expand the understanding of mechanisms of action for extensively studied antibiotics.
History
DepositionMay 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 26, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: 23S ribosomal RNA
5: 16S ribosomal RNA
7: tRNA-Asp (P-site)
8: tRNA-Lys (A-site)
A: 30S ribosomal protein S2
B: 30S ribosomal protein S3
C: 30S ribosomal protein S4
D: 30S ribosomal protein S5
E: 30S ribosomal protein S6
F: 30S ribosomal protein S7
G: 30S ribosomal protein S8
H: 30S ribosomal protein S9
I: 30S ribosomal protein S10
J: 30S ribosomal protein S11
K: 30S ribosomal protein S12
L: 30S ribosomal protein S13
M: 30S ribosomal protein S14 type Z
N: 30S ribosomal protein S15
O: 30S ribosomal protein S16
P: 30S ribosomal protein S17
Q: 30S ribosomal protein S18
R: 30S ribosomal protein S19
S: 30S ribosomal protein S20
T: 30S ribosomal protein S21
Y: mRNA
x: 50S ribosomal protein L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,820,424136
Polymers1,817,22126
Non-polymers3,203110
Water362
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 , 5 types, 5 molecules 3578Y

#1: RNA chain 23S ribosomal RNA


Mass: 940911.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)
#2: RNA chain 16S ribosomal RNA


Mass: 491326.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#3: RNA chain tRNA-Asp (P-site)


Mass: 24136.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#4: RNA chain tRNA-Lys (A-site)


Mass: 24401.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: GenBank: 26117688
#25: RNA chain mRNA


Mass: 6698.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria)

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30S ribosomal protein ... , 20 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#5: Protein 30S ribosomal protein S2


Mass: 33468.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75560
#6: Protein 30S ribosomal protein S3


Mass: 30657.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P41205
#7: Protein 30S ribosomal protein S4


Mass: 23817.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P46775
#8: Protein 30S ribosomal protein S5


Mass: 24138.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50301
#9: Protein 30S ribosomal protein S6


Mass: 25430.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75543
#10: Protein 30S ribosomal protein S7


Mass: 17897.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75545
#11: Protein 30S ribosomal protein S8


Mass: 15903.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50304
#12: Protein 30S ribosomal protein S9


Mass: 15149.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75179
#13: Protein 30S ribosomal protein S10


Mass: 12226.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75581
#14: Protein 30S ribosomal protein S11


Mass: 12709.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50296
#15: Protein 30S ribosomal protein S12


Mass: 15666.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75546
#16: Protein 30S ribosomal protein S13


Mass: 14209.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50297
#17: Protein 30S ribosomal protein S14 type Z


Mass: 6901.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50305
#18: Protein 30S ribosomal protein S15


Mass: 9921.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75173
#19: Protein 30S ribosomal protein S16


Mass: 10806.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: A0A0H3DLS7
#20: Protein 30S ribosomal protein S17


Mass: 9859.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q50309
#21: Protein 30S ribosomal protein S18


Mass: 12411.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75541
#22: Protein 30S ribosomal protein S19


Mass: 10057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75576
#23: Protein 30S ribosomal protein S20


Mass: 9993.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75237
#24: Protein 30S ribosomal protein S21


Mass: 7539.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P57079

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Protein , 1 types, 1 molecules x

#26: Protein 50S ribosomal protein L31


Mass: 10980.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P78020

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Non-polymers , 6 types, 112 molecules

#27: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#28: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#29: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE


Mass: 102.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N2
#30: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 103 / Source method: obtained synthetically / Formula: Mg
#31: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#32: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Mycoplasma pneumoniae M129 cells treated with chloramphenicol
Type: CELL
Details: Small ribosomal subunit with some elements of the large ribosomal subunit. Focused refinement on 30S subunit of the in situ 70S subunit map.
Entity ID: #1-#26 / Source: NATURAL
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria) / Cellular location: Cytoplasm
Buffer solutionpH: 7.4
Details: The modified Hayflick medium: 14.7g/L Difco PPLO(Becton Dickinson), 20% (v/v) Gibco horse serum(New Zealand origin), 100 mM HEPES-Na; pH 7.4, 1% (w/w) glucose, 0.002% (w/w) phenol red, 1000 U/mL penicillin G.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Mycoplasma pneumoniae M129 cells were grown on gold Quantifoil grids at 37 Celsius in the modified Hayflick medium. Treatment with chloramphenicol at the final concentration of 0.2 mg/ml was ...Details: Mycoplasma pneumoniae M129 cells were grown on gold Quantifoil grids at 37 Celsius in the modified Hayflick medium. Treatment with chloramphenicol at the final concentration of 0.2 mg/ml was performed for about 15 minutes before plunge freezing.
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: Back-side blotting for 2-3 seconds before plunging using a manual plunger without an environmental control chamber.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 3250 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.34 e/Å2 / Avg electron dose per subtomogram: 137 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 1
Details: Gatan K3 camera in non-CDS counting mode, targeted dose rate on camera ~20 e/pixel/second, 10 frames per tilt image, constant exposure time for each tilt, pixel size 1.329A
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1PyTom0.9.7.1volume selection
2Warp1.0.9volume selection
3SerialEM3.9image acquisition
5Warp1.0.9CTF correction
8Coot0.9.8.5model fitting
11RELION3.0.8final Euler assignmentRefine3D
12Warp1.0.9final Euler assignmentWarp/M uses RELION alignment
13RELION3.0.8classificationClass3D to remove bad particles
14Warp1.0.93D reconstructionWarp/M
15PHENIX1.20.1_4487model refinement
CTF correctionDetails: CTF estimation and 3D CTF correction are done in Warp
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30774 / Algorithm: FOURIER SPACE / Details: half maps from Warp/M / Symmetry type: POINT
EM volume selectionNum. of tomograms: 139 / Num. of volumes extracted: 30774
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17OOC

7ooc

17OOC1PDBexperimental model
27OOD

7ood

17OOD2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00359798
ELECTRON MICROSCOPYf_angle_d0.56488606
ELECTRON MICROSCOPYf_dihedral_angle_d13.8722196
ELECTRON MICROSCOPYf_chiral_restr0.03211248
ELECTRON MICROSCOPYf_plane_restr0.0065231

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