7OE1

30S ribosomal subunit from E. coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

RbfA Is Involved in Two Important Stages of 30S Subunit Assembly: Formation of the Central Pseudoknot and Docking of Helix 44 to the Decoding Center.

Maksimova, E.M.Korepanov, A.P.Kravchenko, O.V.Baymukhametov, T.N.Myasnikov, A.G.Vassilenko, K.S.Afonina, Z.A.Stolboushkina, E.A.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22116140
  • Primary Citation of Related Structures:  
    7OE0, 7OE1, 7OI0

  • PubMed Abstract: 

    Ribosome biogenesis is a highly coordinated and complex process that requires numerous assembly factors that ensure prompt and flawless maturation of ribosomal subunits. Despite the increasing amount of data collected, the exact role of most assembly factors and mechanistic details of their operation remain unclear, mainly due to the shortage of high-resolution structural information. Here, using cryo-electron microscopy, we characterized 30S ribosomal particles isolated from an Escherichia   coli strain with a deleted gene for the RbfA factor. The cryo-EM maps for pre-30S subunits were divided into six classes corresponding to consecutive assembly intermediates: from the particles with a completely unresolved head domain and unfolded central pseudoknot to almost mature 30S subunits with well-resolved body, platform, and head domains and partially distorted helix 44. The structures of two predominant 30S intermediates belonging to most populated classes obtained at 2.7 Å resolutions indicate that RbfA acts at two distinctive 30S assembly stages: early formation of the central pseudoknot including folding of the head, and positioning of helix 44 in the decoding center at a later stage. Additionally, it was shown that the formation of the central pseudoknot may promote stabilization of the head domain, likely through the RbfA-dependent maturation of the neck helix 28. An update to the model of factor-dependent 30S maturation is proposed, suggesting that RfbA is involved in most of the subunit assembly process.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4B [auth D]205Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5C [auth E]166Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformD [auth F]135Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8E [auth H]129Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11F [auth K]128Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKFAZ83_23205
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12G [auth L]123Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15H [auth O]89Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16I [auth P]82Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17J [auth Q]83Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18K [auth R]74Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20L [auth T]86Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2M [auth B]240Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21N [auth U]71Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3O [auth C]232Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7P [auth G]178Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9Q [auth I]129Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10R [auth J]103Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13S [auth M]117Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14T [auth N]100Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19U [auth S]91Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,542Escherichia coli str. K-12 substr. MG1655
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2.-3874

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-74-20186

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references, Refinement description