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 mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins ...

    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
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MRPL27A [auth 0]148Sus scrofa domesticusMutation(s): 0 
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Entity ID: 2
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MRPL28B [auth 1]256Sus scrofa domesticusMutation(s): 0 
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Entity ID: 3
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MRPL47C [auth 2]252Sus scrofa domesticusMutation(s): 0 
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Entity ID: 4
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MRPL30D [auth 3]161Sus scrofa domesticusMutation(s): 0 
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Entity ID: 5
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MRPL32E [auth 5]146Sus scrofa domesticusMutation(s): 0 
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Entity ID: 6
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MRPL33F [auth 6]65Sus scrofa domesticusMutation(s): 0 
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MRPL34G [auth 7]95Sus scrofa domesticusMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 8
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MRPL35H [auth 8]188Sus scrofa domesticusMutation(s): 0 
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Entity ID: 9
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MRPL36I [auth 9]100Sus scrofa domesticusMutation(s): 0 
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MRPL2L [auth D]306Sus scrofa domesticusMutation(s): 0 
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Entity ID: 13
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MRPL3M [auth E]399Sus scrofa domesticusMutation(s): 0 
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MRPL4N [auth F]224Sus scrofa domesticusMutation(s): 0 
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MRPL9O [auth I]268Sus scrofa domesticusMutation(s): 0 
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MRPL13P [auth N]178Sus scrofa domesticusMutation(s): 0 
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MRPL14Q [auth O]145Sus scrofa domesticusMutation(s): 0 
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MRPL15R [auth P]288Sus scrofa domesticusMutation(s): 0 
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MRPL16S [auth Q]208Sus scrofa domesticusMutation(s): 0 
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MRPL17T [auth R]169Sus scrofa domesticusMutation(s): 0 
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MRPL18U [auth S]180Sus scrofa domesticusMutation(s): 0 
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MRPL19V [auth T]292Sus scrofa domesticusMutation(s): 0 
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Entity ID: 23
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MRPL20W [auth U]132Sus scrofa domesticusMutation(s): 0 
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MRPL21X [auth V]207Sus scrofa domesticusMutation(s): 0 
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MRPL22Y [auth W]134Sus scrofa domesticusMutation(s): 0 
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MRPL23Z [auth X]87Sus scrofa domesticusMutation(s): 0 
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Entity ID: 27
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MRPL24AA [auth Y]216Sus scrofa domesticusMutation(s): 0 
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Entity ID: 28
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MRPL38BA [auth b]380Sus scrofa domesticusMutation(s): 0 
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Entity ID: 29
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MRPL39CA [auth c]301Sus scrofa domesticusMutation(s): 0 
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Entity ID: 30
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MRPL44DA [auth h]298Sus scrofa domesticusMutation(s): 0 
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Entity ID: 31
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MRPL45EA [auth i]312Sus scrofa domesticusMutation(s): 0 
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Entity ID: 32
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MRPL49FA [auth l]166Sus scrofa domesticusMutation(s): 0 
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Entity ID: 33
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MRPL52GA [auth o]56Sus scrofa domesticusMutation(s): 0 
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Entity ID: 34
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ICT1HA [auth u]205Sus scrofa domesticusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
UNASSIGNED HELICESIA [auth v],
JA [auth w]
91Sus scrofa domesticusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
THIOREDOXIN FOLDKA [auth x]85Sus scrofa domesticusMutation(s): 0 
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Entity ID: 37
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UNASSIGNED HELICESLA [auth z]426Sus scrofa domesticusMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganismImage
16S Ribosomal RNAJ [auth A]1,570Sus scrofa domesticus
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Entity ID: 11
MoleculeChainsLengthOrganismImage
UNASSIGNED RNAK [auth B]29Sus scrofa domesticus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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MA [auth 5],
NA [auth 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 
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