8C9B

Cryo-EM captures early ribosome assembly in action


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 2]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7P5
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UniProt GroupP0A7P5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4C [auth E]201Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
Explore P60723 
Go to UniProtKB:  P60723
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UniProt GroupP60723
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22D [auth S]110Escherichia coliMutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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UniProt GroupP61175
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24E [auth U]104Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
Explore P60624 
Go to UniProtKB:  P60624
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UniProt GroupP60624
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29F [auth Y]63Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
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UniProt GroupP0A7M6
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONcryoSPARC

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: 2023-04-12
    Changes: Structure summary
  • Version 1.2: 2024-07-24
    Changes: Data collection