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- PDB-7ooc: Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol... -

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Basic information

Entry
Database: PDB / ID: 7ooc
TitleMycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol-treated cells
Components
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
KeywordsRIBOSOME / In-cell cryo-electron tomography chloramphenicol-treated sub-tomogram analysis
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein S14, type Z / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type ...Ribosomal protein S14, type Z / Ribosomal protein S21 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / 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 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S2 signature 2. / 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 / K Homology domain / K homology RNA-binding domain / 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 S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / 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 S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e
Similarity search - Domain/homology
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 ...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 / 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 speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.7 Å
AuthorsXue, L. / Lenz, S. / Rappsilber, J. / Mahamid, J.
Funding support Germany, United Kingdom, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)426290502 Germany
Wellcome Trust103139 United Kingdom
Wellcome Trust203149 United Kingdom
Citation
Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#1: Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#2: Journal: Biorxiv / Year: 2021
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Authors: Xue, L. / Lenz, S. / Zimmermann-Kogadeeva, M. / Tegunov, D. / Cramer, P. / Bork, P. / Rappsilber, J. / Mahamid, J.
History
DepositionMay 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 30S ribosomal protein S3
D: 30S ribosomal protein S5
F: 30S ribosomal protein S7
A: 30S ribosomal protein S2
H: 30S ribosomal protein S9
J: 30S ribosomal protein S11
C: 30S ribosomal protein S4
S: 30S ribosomal protein S20
O: 30S ribosomal protein S16
K: 30S ribosomal protein S12
M: 30S ribosomal protein S14 type Z
I: 30S ribosomal protein S10
L: 30S ribosomal protein S13
N: 30S ribosomal protein S15
R: 30S ribosomal protein S19
T: 30S ribosomal protein S21
G: 30S ribosomal protein S8
Q: 30S ribosomal protein S18
E: 30S ribosomal protein S6
P: 30S ribosomal protein S17
5: 16S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)810,14023
Polymers810,01021
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein 30S ribosomal protein S3


Mass: 30657.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P41205
#2: Protein 30S ribosomal protein S5


Mass: 24138.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50301
#3: Protein 30S ribosomal protein S7


Mass: 17897.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75545
#4: Protein 30S ribosomal protein S2


Mass: 33468.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75560
#5: Protein 30S ribosomal protein S9


Mass: 15149.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75179
#6: Protein 30S ribosomal protein S11


Mass: 12709.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50296
#7: Protein 30S ribosomal protein S4


Mass: 23817.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P46775
#8: Protein 30S ribosomal protein S20


Mass: 9993.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75237
#9: Protein 30S ribosomal protein S16


Mass: 10806.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: A0A0H3DLS7
#10: Protein 30S ribosomal protein S12


Mass: 15666.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75546
#11: Protein 30S ribosomal protein S14 type Z


Mass: 6901.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50305
#12: Protein 30S ribosomal protein S10


Mass: 12226.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75581
#13: Protein 30S ribosomal protein S13


Mass: 14209.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50297
#14: Protein 30S ribosomal protein S15


Mass: 9921.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75173
#15: Protein 30S ribosomal protein S19


Mass: 10057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75576
#16: Protein 30S ribosomal protein S21


Mass: 7539.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P57079
#17: Protein 30S ribosomal protein S8


Mass: 15903.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50304
#18: Protein 30S ribosomal protein S18


Mass: 12411.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75541
#19: Protein 30S ribosomal protein S6


Mass: 25430.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75543
#20: Protein 30S ribosomal protein S17


Mass: 9859.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50309

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RNA chain / Non-polymers , 2 types, 3 molecules 5

#21: RNA chain 16S rRNA


Mass: 491243.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129
#22: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: cryo-electron tomograms of chloramphenicol-treated Mycoplasma pneumoniae cells
Type: RIBOSOME
Details: ribosome sub-tomograms extracted in silico from cell tomograms, focused refinement on 30S
Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Mycoplasma pneumoniae M129 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Mycoplasma pneumoniae M129 cells grown on gold Quantifoil grids at 37 degrees Celsius before plunge freezing. Quick wash with PBS solution containing gold fiducial beads before blotting.
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: back-side blotting for 2-3 second before plunging manual plunger without an environmental 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: 81000 X / Nominal defocus max: 3750 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
9Coot0.9model refinement
10PHENIX1.18model refinementphenix real-space refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17890
Details: Map generated by focused refinement on the 30S subunit in M
Symmetry type: POINT
EM volume selectionNum. of tomograms: 65 / Num. of volumes extracted: 17890
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
13J9W

3j9w

3J9W1
25MMJ

5mmj

q5MMJ2
34YBB

4ybb

54YBB3

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