4V1A | pdb_00004v1a

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 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 563.89 kDa 
  • Atom Count: 31,917 
  • Modeled Residue Count: 3,936 
  • Deposited Residue Count: 4,946 
  • Unique protein chains: 23

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML37, MRPL37A [auth a]423Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BIV6 (Sus scrofa)
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UniProt GroupA0A287BIV6
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Reference Sequence
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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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML39, MRPL39C [auth c]334Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BI43 (Sus scrofa)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML40, MRPL40D [auth d]206Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2R2V2 (Sus scrofa)
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UniProt GroupA0A5G2R2V2
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML41, MRPL41E [auth e]135Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1F1K9 (Sus scrofa)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML42, MRPL42F [auth f]142Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8C5VHE0 (Microcebus murinus)
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML43, MRPL43G [auth g]159Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S8U4 (Sus scrofa)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML44, MRPL44H [auth h]332Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML45, MRPL45I [auth i]312Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LGM5 (Sus scrofa)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML46, MRPL46J [auth j]279Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML48, MRPL48K [auth k]212Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML49, MRPL49L [auth l]166Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V1G7 (Sus scrofa)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML50, MRPL50M [auth m]159Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML51, MRPL51N [auth n]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1P1C8 (Sus scrofa)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML52, MRPL52O [auth o]124Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S9B7 (Sus scrofa)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML53, MRPL53P [auth p]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for Q2HJF1 (Bos taurus)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML54, MRPL54Q [auth q]138Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480PHA9 (Sus scrofa)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML63, MRPL57, MRP63R [auth t]102Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BP93 (Sus scrofa)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML62, MRPL58, ICT1S [auth u]205Sus scrofaMutation(s): 0 
EC: 3.1.1.29
UniProt
Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML64, MRPL59, CRIF1T [auth v]222Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZXA6 (Sus scrofa)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML65, MRPS30U [auth w]433Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480QIM3 (Sus scrofa)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN ML66, MRPS18AV [auth x]196Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2R1G5 (Sus scrofa)
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
UNASSIGNED SECONDARY STRUCTURE ELEMENTSW [auth z]47Sus scrofaMutation(s): 0 
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Reference Sequence

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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
F [auth f]L-PEPTIDE LINKINGC4 H9 N O2

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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
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations