4V1A

Structure of the large subunit of the mammalian mitoribosome, part 2 of 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

The Complete Structure of the Large Subunit of the Mammalian Mitochondrial Ribosome

Greber, B.J.Boehringer, D.Leibundgut, M.Bieri, P.Leitner, A.Schmitz, N.Aebersold, R.Ban, N.

(2014) Nature 515: 283

  • DOI: https://doi.org/10.1038/nature13895
  • Primary Citation of Related Structures:  
    4V19, 4V1A

  • PubMed Abstract: 

    Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML37, MRPL37A [auth a]423Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML38, MRPL38B [auth b]380Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RW03 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML39, MRPL39C [auth c]334Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML40, MRPL40D [auth d]206Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML41, MRPL41E [auth e]135Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML42, MRPL42F [auth f]142Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML43, MRPL43G [auth g]159Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML44, MRPL44H [auth h]332Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML45, MRPL45I [auth i]312Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML46, MRPL46J [auth j]279Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML48, MRPL48K [auth k]212Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML49, MRPL49L [auth l]166Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML50, MRPL50M [auth m]159Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML51, MRPL51N [auth n]128Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML52, MRPL52O [auth o]124Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML53, MRPL53P [auth p]112Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML54, MRPL54Q [auth q]138Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63R [auth t]102Sus scrofaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML62, MRPL58, ICT1S [auth u]205Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1T [auth v]222Sus scrofaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML65, MRPS30U [auth w]433Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML66, MRPS18AV [auth x]196Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RRH6 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
UNASSIGNED SECONDARY STRUCTURE ELEMENTSW [auth z]47Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
X [auth x]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1.9
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2014-11-19
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Data collection
  • Version 1.4: 2019-10-02
    Changes: Data collection, Other