8C94

Cryo-EM captures early ribosome assembly in action


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM captures early ribosome assembly in action.

Qin, B.Lauer, S.M.Balke, A.Vieira-Vieira, C.H.Burger, J.Mielke, T.Selbach, M.Scheerer, P.Spahn, C.M.T.Nikolay, R.

(2023) Nat Commun 14: 898-898

  • DOI: https://doi.org/10.1038/s41467-023-36607-9
  • Primary Citation of Related Structures:  
    8C8X, 8C8Y, 8C8Z, 8C90, 8C91, 8C92, 8C93, 8C94, 8C95, 8C96, 8C97, 8C98, 8C99, 8C9A, 8C9B, 8C9C

  • PubMed Abstract: 

    Ribosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit, we exploited a minimal in vitro reconstitution system using purified ribosomal components and scalable reaction conditions. Time-limited assembly assays combined with cryo-EM analysis visualizes the structurally complex assembly pathway starting with a particle consisting of ordered density for only ~500 nucleotides of 23S rRNA domain I and three ribosomal proteins. In addition, our structural analysis reveals that early 50S assembly occurs in a domain-wise fashion, while late 50S assembly proceeds incrementally. Furthermore, we find that both ribosomal proteins and folded rRNA helices, occupying surface exposed regions on pre-50S particles, induce, or stabilize rRNA folds within adjacent regions, thereby creating cooperativity.


  • Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Escherichia coliMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth L]144Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17K [auth N]127Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L18L [auth O]117Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19M [auth P]115Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20N [auth Q]118Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21O [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22P [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L24Q [auth U]104Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25R [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L27S [auth W]85Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29T [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30U [auth Z]59Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
23S rRNAC [auth A]2,904Escherichia coli
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNAD [auth B]119Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3
MODEL REFINEMENTPHENIX1.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany16GW0300

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Data collection