4V19

Structure of the large subunit of the mammalian mitoribosome, part 1 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 2.2 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
  • 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 ...

    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 LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL27M, MRPL27A [auth 0]148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
UniProt
Find proteins for F1RT79 (Sus scrofa)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL28M, MRPL28B [auth 1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL18
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL29M, MRPL47C [auth 2]252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
UniProt
Find proteins for F1SGC7 (Sus scrofa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL30M, MRPL30D [auth 3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
UniProt
Find proteins for F1STE5 (Sus scrofa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL31M, MRPL55E [auth 4]126Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL32M, MRPL32F [auth 5]188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
UniProt
Find proteins for I3LTC4 (Sus scrofa)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL33M, MRPL33G [auth 6]65Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL34M, MRPL34H [auth 7]95Sus scrofaMutation(s): 0 
UniProt
Find proteins for W5IDC1 (Sus scrofa domesticus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL35M, MRPL35I [auth 8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL36M, MRPL36J [auth 9]100Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL2M, MRPL2N [auth D]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
UniProt
Find proteins for F1RRN2 (Sus scrofa)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL3M, MRPL3O [auth E]348Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL4M, MRPL4P [auth F]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
UniProt
Find proteins for F1S3J8 (Sus scrofa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL9M, MRPL9Q [auth I]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
UniProt
Find proteins for I3LR45 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL10M, MRPL10R [auth J]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
UniProt
Find proteins for F1RWJ0 (Sus scrofa)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL11M, MRPL11S [auth K]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
UniProt
Find proteins for F1RU54 (Sus scrofa)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL13M, MRPL13T [auth N]178Sus scrofaMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL14M, MRPL14U [auth O]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
UniProt
Find proteins for F1RQV7 (Sus scrofa)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL15M, MRPL15V [auth P]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
UniProt
Find proteins for F1RSH0 (Sus scrofa)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL16M, MRPL16W [auth Q]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
UniProt
Find proteins for F1RI89 (Sus scrofa)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL17M, MRPL17X [auth R]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
UniProt
Find proteins for F1RMQ4 (Sus scrofa)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL18M, MRPL18Y [auth S]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
UniProt
Find proteins for A0A0R4J8D5 (Sus scrofa)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL19M, MRPL19Z [auth T]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL20M, MRPL20AA [auth U]149Sus scrofaMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN BL21M, MRPL21BA [auth V]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL22M, MRPL22CA [auth W]210Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL23M, MRPL23DA [auth X]150Sus scrofaMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
MITORIBOSOMAL PROTEIN UL24M, MRPL24EA [auth Y]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
UniProt
Find proteins for F1RHJ1 (Sus scrofa)
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Entity ID: 11
MoleculeChainsLengthOrganismImage
MITORIBOSOMAL 16S RRNAK [auth A]1570Sus scrofa
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Entity ID: 12
MoleculeChainsLengthOrganismImage
MITORIBOSOMAL CP TRNAL [auth B]62Sus scrofa
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    TRNAM [auth C], FA [auth Z]3Sus scrofa
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    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    GA [auth 5], HA [auth 9]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , BB [auth A] , BC [auth A] , 
    AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PG [auth D],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth D],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth P],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth P],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth Q],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth R],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-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  (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 2.0: 2017-08-02
      Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
    • Version 2.1: 2019-10-02
      Changes: Data collection, Derived calculations, Other
    • Version 2.2: 2019-10-23
      Changes: Data collection, Other