7PIQ

70S ribosome with A- and P-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Visualizing translation dynamics at atomic detail inside a bacterial cell.

Xue, L.Lenz, S.Zimmermann-Kogadeeva, M.Tegunov, D.Cramer, P.Bork, P.Rappsilber, J.Mahamid, J.

(2022) Nature 610: 205-211

  • DOI: https://doi.org/10.1038/s41586-022-05255-2
  • Primary Citation of Related Structures:  
    7OOC, 7OOD, 7P6Z, 7PAH, 7PAI, 7PAJ, 7PAK, 7PAL, 7PAM, 7PAN, 7PAO, 7PAQ, 7PAR, 7PAS, 7PAT, 7PAU, 7PH9, 7PHA, 7PHB, 7PHC, 7PI8, 7PI9, 7PIA, 7PIB, 7PIC, 7PIO, 7PIP, 7PIQ, 7PIR, 7PIS, 7PIT

  • PubMed Abstract: 

    Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells 1 . Here we use advances in cryo-electron tomography and sub-tomogram analysis 2,3 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 4 . 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.


  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34A [auth 0]48Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35B [auth 1]59Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36C [auth 2]37Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2D [auth A]294Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3E [auth B]273Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4F [auth C]205Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5G [auth D]219Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6H [auth E]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7I [auth F]155Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8J [auth G]142Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9K [auth H]132Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10L [auth I]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11M [auth J]121Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12N [auth K]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13O [auth L]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZP [auth M]61Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15Q [auth N]86Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16R [auth O]94Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17S [auth P]85Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18T [auth Q]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19U [auth R]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20V [auth S]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21W [auth T]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth a]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth b]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth c]212Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth d]180Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth e]184Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth f]149Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10DA [auth g]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11EA [auth h]137Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13FA [auth i]146Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14GA [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15HA [auth k]151Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16IA [auth l]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17JA [auth m]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18KA [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19LA [auth o]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20MA [auth p]127Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21NA [auth q]100Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22OA [auth r]159Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PA [auth s]237Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24QA [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth u]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28SA [auth v]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75171 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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UniProt GroupP75171
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29TA [auth w]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50310 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31UA [auth x]97Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78020 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth y]57Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75238 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1WA [auth z]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78015 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 50
MoleculeChains LengthOrganismImage
23S ribosomal RNAXA [auth 3]2,907Mycoplasmoides pneumoniae M129
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Entity ID: 51
MoleculeChains LengthOrganismImage
5S ribosomal RNAYA [auth 4]108Mycoplasmoides pneumoniae M129
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Entity ID: 52
MoleculeChains LengthOrganismImage
16S ribosomal RNAZA [auth 5]1,520Mycoplasmoides pneumoniae M129
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Entity ID: 53
MoleculeChains LengthOrganismImage
tRNA-PheAB [auth 6],
BB [auth 7]
76Mycoplasmoides pneumoniae M129
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United Kingdom760067
German Research Foundation (DFG)United Kingdom426290502
Wellcome TrustUnited Kingdom103139
Wellcome TrustUnited Kingdom203149

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references