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: 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 m ...

    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

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL270148Sus scrofa domesticusMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL281256Sus scrofa domesticusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL472252Sus scrofa domesticusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL303161Sus scrofa domesticusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL325146Sus scrofa domesticusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL33665Sus scrofa domesticusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL34795Sus scrofa domesticusMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL358188Sus scrofa domesticusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL369100Sus scrofa domesticusMutation(s): 0 
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Entity ID: 12
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MRPL2D306Sus scrofa domesticusMutation(s): 0 
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Entity ID: 13
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MRPL3E399Sus scrofa domesticusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL4F224Sus scrofa domesticusMutation(s): 0 
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Entity ID: 15
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MRPL9I268Sus scrofa domesticusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL13N178Sus scrofa domesticusMutation(s): 0 
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Entity ID: 17
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MRPL14O145Sus scrofa domesticusMutation(s): 0 
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Entity ID: 18
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MRPL15P288Sus scrofa domesticusMutation(s): 0 
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Entity ID: 19
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MRPL16Q208Sus scrofa domesticusMutation(s): 0 
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Entity ID: 20
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MRPL17R169Sus scrofa domesticusMutation(s): 0 
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Entity ID: 21
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MRPL18S180Sus scrofa domesticusMutation(s): 0 
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Entity ID: 22
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MRPL19T292Sus scrofa domesticusMutation(s): 0 
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Entity ID: 24
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MRPL21V207Sus scrofa domesticusMutation(s): 0 
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Entity ID: 25
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MRPL22W134Sus scrofa domesticusMutation(s): 0 
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Entity ID: 26
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MRPL23X87Sus scrofa domesticusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL24Y216Sus scrofa domesticusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL38b380Sus scrofa domesticusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL39c301Sus scrofa domesticusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL44h298Sus scrofa domesticusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL45i312Sus scrofa domesticusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL49l166Sus scrofa domesticusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL52o56Sus scrofa domesticusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
ICT1u205Sus scrofa domesticusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
UNASSIGNED HELICESvw91Sus scrofa domesticusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
THIOREDOXIN FOLDx85Sus scrofa domesticusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
MRPL20U132Sus scrofa domesticusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
UNASSIGNED HELICESz426Sus scrofa domesticusMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAA1570Sus scrofa domesticus
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Entity ID: 11
MoleculeChainsLengthOrganismImage
UNASSIGNED RNAB29Sus scrofa domesticus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
5, 9
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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