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 9SK4 | pdb_00009sk4

Model of M. pneumoniae 30S IF3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.2 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: 787.11 kDa 
  • Atom Count: 52,521 
  • Modeled Residue Count: 4,126 
  • Deposited Residue Count: 4,139 
  • Unique protein chains: 21
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2B [auth A]249Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75560 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75560 
Go to UniProtKB:  P75560
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UniProt GroupP75560
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3C [auth B]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41205 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P41205 
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UniProt GroupP41205
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4D [auth C]203Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P46775 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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UniProt GroupP46775
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5E [auth D]153Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50301 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6F [auth E]167Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75543 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75543 
Go to UniProtKB:  P75543
Entity Groups
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7G [auth F]154Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75545 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75545 
Go to UniProtKB:  P75545
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8H [auth G]141Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50304 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore Q50304 
Go to UniProtKB:  Q50304
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9I [auth H]128Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75179 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10J [auth I]101Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75581 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11K [auth J]114Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50296 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12L [auth K]136Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75546 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75546 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13M [auth L]118Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50297 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14N [auth M]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50305 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore Q50305 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15O [auth N]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75173 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75173 
Go to UniProtKB:  P75173
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16P [auth O]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for A0A0H3DLS7 (Mycoplasmoides pneumoniae (strain ATCC 15531 / DSM 23978 / CIP 103766 / NBRC 14401 / NCTC 10119 / FH))
Explore A0A0H3DLS7 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17Q [auth P]83Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50309 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity Groups
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18R [auth Q]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75541 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75541 
Go to UniProtKB:  P75541
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19S [auth R]84Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75576 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75576 
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS20T [auth S]77Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75237 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P75237 
Go to UniProtKB:  P75237
Entity Groups
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UniProt GroupP75237
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21U [auth T]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P57079 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P57079 
Go to UniProtKB:  P57079
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor IF-3V [auth U]163Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78024 (Mycoplasmoides pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
Explore P78024 
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UniProt GroupP78024
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth 5]1,505Mycoplasmoides pneumoniae M129
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.2 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