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 9SKF | pdb_00009skf

Model of M. pneumoniae 70S membrane complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

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This is version 1.1 of the entry. See complete history. 

Literature

Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.

Dobbs, J.M., Jensen, R.K., Mahamid, J.

(2026) Cell 

  • DOI: https://doi.org/10.1016/j.cell.2026.08.054
  • Primary Citation Related Structures: 
    9SK2, 9SK4, 9SK5, 9SK6, 9SK7, 9SK8, 9SK9, 9SKA, 9SKB, 9SKC, 9SKD, 9SKE, 9SKF, 9SL4, 9SL5, 9SL6, 9SL7

  • PubMed Abstract: 

    Translation is a central process in gene expression. Its regulation is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk to processes such as transcription or translocation. Here, we used cryo-electron tomography of native and antibiotic-perturbed Mycoplasma pneumoniae cells to resolve 140 maps that recapitulate bacterial translation during the initiation, elongation, and recycling phases. We visualized multiple transcription-translation complexes, allowing us to propose a threading-based translation reinitiation mechanism and to provide structural evidence for a long-hypothesized supercomplex that coordinates transcription, translation, and membrane attachment. We resolved abundant membrane-associated large ribosomal subunits and suggest that dissociation from membranes depends on the conditional initiation of new translation, consistent with a potentially conserved mechanism in mammalian cells. This work visualizes the multilayered control of bacterial translation and demonstrates the power of in-cell structural biology to investigate regulatory circuits in gene expression.


  • Organizational Affiliation: 
    • Molecular Systems Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 2,276.54 kDa 
  • Atom Count: 152,772 
  • Modeled Residue Count: 11,524 
  • Deposited Residue Count: 11,611 
  • Unique protein chains: 51
  • Unique nucleic acid chains: 4

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34A [auth 0]47Mycoplasmoides 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: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
SecDFH [auth 8]944Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2I [auth A]240Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3J [auth B]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4K [auth C]203Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5L [auth D]153Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6M [auth E]167Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7N [auth F]154Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8O [auth G]141Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9P [auth H]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10Q [auth I]101Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11R [auth J]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12S [auth K]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13T [auth L]118Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14U [auth M]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15V [auth N]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16W [auth O]80Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17X [auth P]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18Y [auth Q]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19Z [auth R]84Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20AA [auth S]77Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21BA [auth T]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10CA [auth U]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL12DA [auth V],
EA [auth W],
FA [auth X],
GA [auth Y]
29Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2HA [auth a]285Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3IA [auth b]229Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4JA [auth c]210Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5KA [auth d]175Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6LA [auth e]176Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9MA [auth f]145Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11NA [auth h]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13OA [auth i]144Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PA [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15QA [auth k]148Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16RA [auth l]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17SA [auth m]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18TA [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19UA [auth o]115Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20VA [auth p]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21WA [auth q]99Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22XA [auth r]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23YA [auth s]92Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24ZA [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27AB [auth u]86Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28BB [auth v]63Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Go to UniProtKB:  P75171
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UniProt GroupP75171
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Reference Sequence
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29CB [auth w]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50310 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore Q50310 
Go to UniProtKB:  Q50310
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31DB [auth x]44Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78020 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Go to UniProtKB:  P78020
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Entity ID: 54
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32EB [auth y]56Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75238 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75238 
Go to UniProtKB:  P75238
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Entity ID: 55
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AFB [auth z]50Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78015 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P78015 
Go to UniProtKB:  P78015
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UniProt GroupP78015
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Entity ID: 4
MoleculeChains LengthOrganismImage
23S ribosomal RNAD [auth 3]2,893Mycoplasmoides pneumoniae M129
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S ribosomal RNAE [auth 4]108Mycoplasmoides pneumoniae M129
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S ribosomal RNAF [auth 5]1,505Mycoplasmoides pneumoniae M129
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Entity ID: 7
MoleculeChains LengthOrganismImage
tRNA-PheG [auth 7]76Mycoplasmoides pneumoniae M129
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.60 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONM

Structure Validation

Currently 9SKF does not have a validation slider image.



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chan Zuckerberg InitiativeUnited States2021-234620
Independent Research Fund Denmark - Medical SciencesDenmark0106-00010A

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-23
    Type: Initial release
  • Version 1.1: 2026-10-07
    Changes: Database references