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- PDB-7pat: free 50S in untreated Mycoplasma pneumoniae cells -

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Basic information

Entry
Database: PDB / ID: 7pat
Titlefree 50S in untreated Mycoplasma pneumoniae cells
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / In-cell cryo-electron tomography / sub-tomogram analysis / translation intermediate state
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / 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 L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesMycoplasma pneumoniae M129 (bacteria)
Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsXue, L. / Lenz, S. / Rappsilber, J. / Mahamid, J.
Funding support Germany, United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council (ERC)760067 Germany
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: 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
DepositionJul 30, 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 / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L34
1: 50S ribosomal protein L35
2: 50S ribosomal protein L36
a: 50S ribosomal protein L2
b: 50S ribosomal protein L3
c: 50S ribosomal protein L4
d: 50S ribosomal protein L5
e: 50S ribosomal protein L6
f: 50S ribosomal protein L9
g: 50S ribosomal protein L10
h: 50S ribosomal protein L11
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16
m: 50S ribosomal protein L17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L27
v: 50S ribosomal protein L28
w: 50S ribosomal protein L29
x: 50S ribosomal protein L31
y: 50S ribosomal protein L32
z: 50S ribosomal protein L33 1
3: 23S ribosomal RNA
4: 5S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)1,411,99431
Polymers1,411,99431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area157670 Å2
ΔGint-1221 kcal/mol
Surface area485230 Å2

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 012abcdefghijklmnopqrstuvwxyz

#1: Protein/peptide 50S ribosomal protein L34 /


Mass: 5616.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P78006
#2: Protein 50S ribosomal protein L35 /


Mass: 6793.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75447
#3: Protein/peptide 50S ribosomal protein L36 /


Mass: 4400.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P52864
#4: Protein 50S ribosomal protein L2 /


Mass: 31966.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75577
#5: Protein 50S ribosomal protein L3 /


Mass: 31298.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75580
#6: Protein 50S ribosomal protein L4 /


Mass: 23632.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75579
#7: Protein 50S ribosomal protein L5 /


Mass: 20270.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50306
#8: Protein 50S ribosomal protein L6 /


Mass: 20624.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50303
#9: Protein 50S ribosomal protein L9 /


Mass: 17185.037 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: P75540
#10: Protein 50S ribosomal protein L10 /


Mass: 17645.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75240
#11: Protein 50S ribosomal protein L11 /


Mass: 14803.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75550
#12: Protein 50S ribosomal protein L13 /


Mass: 16821.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75178
#13: Protein 50S ribosomal protein L14 /


Mass: 13478.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50308
#14: Protein 50S ribosomal protein L15 /


Mass: 16768.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50300
#15: Protein 50S ribosomal protein L16 /


Mass: 15646.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P41204
#16: Protein 50S ribosomal protein L17 /


Mass: 14270.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q59547
#17: Protein 50S ribosomal protein L18 /


Mass: 13073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50302
#18: Protein 50S ribosomal protein L19 /


Mass: 13870.327 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: P75133
#19: Protein 50S ribosomal protein L20 /


Mass: 14742.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P78023
#20: Protein 50S ribosomal protein L21 /


Mass: 11664.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P78026
#21: Protein 50S ribosomal protein L22 /


Mass: 17355.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75575
#22: Protein 50S ribosomal protein L23 /


Mass: 25892.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75578
#23: Protein 50S ribosomal protein L24 /


Mass: 12461.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50307
#24: Protein 50S ribosomal protein L27 /


Mass: 11527.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75458
#25: Protein 50S ribosomal protein L28 /


Mass: 7549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75171
#26: Protein 50S ribosomal protein L29 /


Mass: 13003.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: Q50310
#27: Protein 50S ribosomal protein L31 /


Mass: 10980.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P78020
#28: Protein 50S ribosomal protein L32 /


Mass: 6641.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P75238
#29: Protein 50S ribosomal protein L33 1 / Ribosome


Mass: 6298.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / Strain: ATCC 29342 / M129 / References: UniProt: P78015

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RNA chain , 2 types, 2 molecules 34

#30: RNA chain 23S ribosomal RNA /


Mass: 940911.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria)
#31: RNA chain 5S ribosomal RNA /


Mass: 34796.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria)

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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 untreated Mycoplasma pneumoniae cells
Type: CELL
Details: Ribosome sub-tomograms extracted in silico from tomograms of intact cell, refinement with a 70S mask
Entity ID: all / 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 Celsius before plunge freezing.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: back-side blotting for 2-3 seconds before plunging using a 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 FIELDBright-field microscopy / 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
2Warp3.0.7 beta or 3.0.9volume selection
3SerialEMimage acquisition
5RELION3.0.8CTF correction
8PHENIX1.18model fitting
11RELION3.0.8final Euler assignment
12RELION3.0.8classification
13RELION3.0.83D reconstruction
14PHENIX1.18model refinementreal-space refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15954 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 356 / Num. of volumes extracted: 77539
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7OOD

7ood

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