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 9SKD | pdb_00009skd

Model of M. pneumoniae 50S membrane complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

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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: 1,496.37 kDa 
  • Atom Count: 100,646 
  • Modeled Residue Count: 7,551 
  • Deposited Residue Count: 7,608 
  • Unique protein chains: 31
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34A [auth 0]47Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78006 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35B [auth 1]59Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75447 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36C [auth 2]37Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P52864 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
SecDFG [auth 9]944Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75387 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L10H [auth A]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75240 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL12I [auth B],
J [auth C],
K [auth D],
L [auth E]
29Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75239 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2M [auth a]285Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75577 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3N [auth b]229Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75580 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4O [auth c]210Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75579 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5P [auth d]175Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50306 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6Q [auth e]176Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50303 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9R [auth f]145Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75540 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL11S [auth h]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75550 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13T [auth i]144Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75178 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14U [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50308 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15V [auth k]148Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50300 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16W [auth l]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41204 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17X [auth m]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q59547 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18Y [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50302 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19Z [auth o]115Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75133 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20AA [auth p]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78023 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21BA [auth q]99Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78026 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22CA [auth r]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75575 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23DA [auth s]92Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75578 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24EA [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50307 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27FA [auth u]86Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75458 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28GA [auth v]63Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75171 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29HA [auth w]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50310 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31IA [auth x]44Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78020 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32JA [auth y]56Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75238 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33AKA [auth z]50Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78015 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 4
MoleculeChains LengthOrganismImage
23S ribosomal RNAD [auth 3]2,878Mycoplasmoides pneumoniae M129
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Entity ID: 5
MoleculeChains LengthOrganismImage
5S ribosomal RNAE [auth 4]105Mycoplasmoides pneumoniae M129
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Entity ID: 6
MoleculeChains LengthOrganismImage
tRNA-PheF [auth 8]51Mycoplasmoides pneumoniae M129
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONM

Structure Validation

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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