4CE4

39S large subunit of the porcine mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Architecture of the Large Subunit of the Mammalian Mitochondrial Ribosome.

Greber, B.J.Boehringer, D.Leitner, A.Bieri, P.Voigts-Hoffmann, F.Erzberger, J.P.Leibundgut, M.Aebersold, R.Ban, N.

(2014) Nature 505: 515

  • DOI: https://doi.org/10.1038/nature12890
  • Primary Citation of Related Structures:  
    4CE4

  • PubMed Abstract: 

    Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.


  • Organizational Affiliation

    1] Department of Biology, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, ETH Zurich, CH-8093 Zurich, Switzerland [2].


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL27A [auth 0]148Sus scrofa domesticusMutation(s): 0 
UniProt
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UniProt GroupA0A4X1U0F6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL28B [auth 1]256Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL47C [auth 2]252Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL30D [auth 3]161Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A8D1MIP3 (Sus scrofa)
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UniProt GroupA0A8D1MIP3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL32E [auth 5]146Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL33F [auth 6]65Sus scrofa domesticusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL34G [auth 7]95Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL35H [auth 8]188Sus scrofa domesticusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL36I [auth 9]100Sus scrofa domesticusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL2L [auth D]306Sus scrofa domesticusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL3M [auth E]399Sus scrofa domesticusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL4N [auth F]224Sus scrofa domesticusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL9O [auth I]268Sus scrofa domesticusMutation(s): 0 
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Find proteins for I3LR45 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL13P [auth N]178Sus scrofa domesticusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL14Q [auth O]145Sus scrofa domesticusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL15R [auth P]288Sus scrofa domesticusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL16S [auth Q]208Sus scrofa domesticusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL17T [auth R]169Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL18U [auth S]180Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL19V [auth T]292Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL20W [auth U]132Sus scrofa domesticusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL21X [auth V]207Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL22Y [auth W]134Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL23Z [auth X]87Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL24AA [auth Y]216Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL38BA [auth b]380Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL39CA [auth c]301Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1SHP6 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL44DA [auth h]298Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL45EA [auth i]312Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL49FA [auth l]166Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
MRPL52GA [auth o]56Sus scrofa domesticusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1HA [auth u]205Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
UNASSIGNED HELICESIA [auth v],
JA [auth w]
91Sus scrofa domesticusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
THIOREDOXIN FOLDKA [auth x]85Sus scrofa domesticusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
UNASSIGNED HELICESLA [auth z]426Sus scrofa domesticusMutation(s): 0 
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Entity ID: 10
MoleculeChains LengthOrganismImage
16S Ribosomal RNAJ [auth A]1,570Sus scrofa domesticus
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Entity ID: 11
MoleculeChains LengthOrganismImage
UNASSIGNED RNAK [auth B]29Sus scrofa domesticus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONIMAGIC5
RECONSTRUCTIONRELION
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 2.0: 2017-08-02
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2019-04-10
    Changes: Data collection, Database references