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 5LL6 | pdb_00005ll6

Structure of the 40S ABCE1 post-splitting complex in ribosome recycling and translation initiation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.6 of the entry. See complete history. 

Literature

Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation.

Heuer, A., Gerovac, M., Schmidt, C., Trowitzsch, S., Preis, A., Kotter, P., Berninghausen, O., Becker, T., Beckmann, R., Tampe, R.

(2017) Nat Struct Mol Biol 24: 453-460

  • DOI: https://doi.org/10.1038/nsmb.3396
  • Primary Citation Related Structures: 
    5LL6

  • PubMed Abstract: 

    The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1. Notably, the movement implies a collision with A-site factors, thus explaining the splitting mechanism. Disruption of key interactions in the post-splitting complex impairs cellular homeostasis. Additionally, the structure of a native post-splitting complex reveals ABCE1 to be part of the 43S initiation complex, suggesting a coordination of termination, recycling, and initiation.


  • Organizational Affiliation: 
    • Gene Center and Center of Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.

Macromolecule Content 

  • Total Structure Weight: 991.67 kDa 
  • Atom Count: 55,262 
  • Modeled Residue Count: 4,754 
  • Deposited Residue Count: 5,456 
  • Unique protein chains: 19
  • Unique nucleic acid chains: 1

Macromolecules


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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth P]252Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AC [auth Q]255Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth R]254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE [auth S]261Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX35
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AF [auth T]236Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AG [auth U]190Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AH [auth V]200Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AI [auth W]197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AJ [auth X]156Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13K [auth Y]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-AL [auth Z]137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AM [auth a]87Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AN [auth b]130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AO [auth c]145Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AP [auth d]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-AQ [auth e]119Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AR [auth f]82Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AS [auth g]63Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Translation initiation factor RLI1T [auth h]608Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth 2]1,798Saccharomyces cerevisiae
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references
  • Version 1.5: 2026-08-26
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Advisory, Derived calculations, Structure summary
  • Version 1.6: 2026-09-23
    Changes: Advisory, Derived calculations, Structure summary