8C90

Cryo-EM captures early ribosome assembly in action


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 L25A [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3C [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4D [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13E [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14F [auth K]123Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15G [auth L]144Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17H [auth N]127Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19I [auth P]115Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20J [auth Q]118Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L21K [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22L [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23M [auth T]100Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L24N [auth U]104Escherichia coliMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L29O [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L32P [auth 0]57Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L34Q [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L18R [auth O]117Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L5S [auth F]179Escherichia 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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth W]85Escherichia coliMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3
MODEL REFINEMENTPHENIX1.2

Structure Validation

View Full Validation Report



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