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 

wwPDB Validation 3D Report Full Report


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: 10.1038/nature13895
  • Structures With Same Primary Citation

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML37, MRPL37a423Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML38, MRPL38b380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
Find proteins for F1RW03 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML39, MRPL39c334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
Find proteins for F1SHP6 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML40, MRPL40d206Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML41, MRPL41e135Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML42, MRPL42f142Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML43, MRPL43g159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
Find proteins for F1S8U4 (Sus scrofa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML44, MRPL44h332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML45, MRPL45i312Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML46, MRPL46j279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML48, MRPL48k212Sus scrofaMutation(s): 0 
Gene Names: MRPL48
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML49, MRPL49l166Sus scrofaMutation(s): 0 
Gene Names: MRPL18
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML50, MRPL50m159Sus scrofaMutation(s): 0 
Gene Names: MRPL50
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML51, MRPL51n128Sus scrofaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML52, MRPL52o124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
Find proteins for F1S9B7 (Sus scrofa)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML53, MRPL53p112Sus scrofaMutation(s): 0 
Gene Names: CCDC142
Find proteins for F1SLH8 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML54, MRPL54q138Sus scrofaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63t102Sus scrofaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML62, MRPL58, ICT1u205Sus scrofaMutation(s): 0 
Find proteins for W5IDC0 (Sus scrofa domesticus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1v222Sus scrofaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML65, MRPS30w433Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
MITORIBOSOMAL PROTEIN ML66, MRPS18Ax196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
Find proteins for F1RRH6 (Sus scrofa)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
UNASSIGNED SECONDARY STRUCTURE ELEMENTSz47Sus scrofaMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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x
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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