4ADX

The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Cryo-Em Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6 and Implications for Ribosome Evolution

Greber, B.J.Boehringer, D.Godinic-Mikulcic, V.Crnkovic, A.Ibba, M.Weygand-Durasevic, I.Ban, N.

(2012) J Mol Biol 418: 145

  • DOI: https://doi.org/10.1016/j.jmb.2012.01.018
  • Primary Citation of Related Structures:  
    4ADX

  • PubMed Abstract: 

    Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, Schafmattstrasse 20, ETH Zurich, 8093 Zurich, Switzerland.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RPL37EB [auth 1]57Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RPL39EC [auth 2]50Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RPL44ED [auth 3]92Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RPL34EE [auth 4]123Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RPL40EF [auth 5]129Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPL30EG [auth 6]104Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
RPL14EH [auth 7]126Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RPL2K [auth A]240Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RPL3L [auth B]338Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPL4M [auth C]246Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RPL5N [auth D]177Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RPL6O [auth E]178Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RPL7AEP [auth F]120Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RPLXQ [auth G]78Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
Find proteins for O27647 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RPL10ER [auth H]177Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
AIF6S [auth I]222Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RPL13T [auth J]145Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RPL14U [auth K]132Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RPL15V [auth L]165Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RPL15EW [auth M]196Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RPL18X [auth N]187Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
RPL18EY [auth O]116Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RPL19EZ [auth P]149Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RPL21EAA [auth Q]96Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RPL22BA [auth R]155Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RPL23CA [auth S]85Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24DA [auth T]120Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RPL24EEA [auth U]67Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
RPL29FA [auth V]71Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RPL30GA [auth W]154Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RPL31EHA [auth X]92Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
RPL32EIA [auth Y]241Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RPL37AEJA [auth Z]92Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth 0]2,923Methanothermobacter thermautotrophicus str. Delta H
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Entity ID: 9
MoleculeChains LengthOrganismImage
23S Ribosomal RNA EXPANSION SEGMENTSI [auth 8]133Methanothermobacter thermautotrophicus str. Delta H
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Entity ID: 10
MoleculeChains LengthOrganismImage
5S Ribosomal RNAJ [auth 9]122Methanothermobacter thermautotrophicus str. Delta H
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Other
  • Version 1.2: 2013-03-20
    Changes: Other, Source and taxonomy
  • Version 1.3: 2017-08-23
    Changes: Data collection, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Refinement description