7ODS

State B of the human mitoribosomal large subunit assembly intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Stepwise maturation of the peptidyl transferase region of human mitoribosomes.

Lenarcic, T.Jaskolowski, M.Leibundgut, M.Scaiola, A.Schonhut, T.Saurer, M.Lee, R.G.Rackham, O.Filipovska, A.Ban, N.

(2021) Nat Commun 12: 3671-3671

  • DOI: https://doi.org/10.1038/s41467-021-23811-8
  • Primary Citation of Related Structures:  
    7ODR, 7ODS, 7ODT

  • PubMed Abstract: 

    Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes have diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. The structural basis of the mammalian mitochondrial ribosome assembly is currently not well understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving seven assembly factors. We discover that the NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by the MRM2 methyltransferase and quality control interactions with the conserved mitochondrial GTPase MTG2 that contacts the sarcin-ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1A [auth u]234Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156928 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MIEF1 upstream open reading frame proteinB [auth v]70Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier protein, mitochondrialC [auth w]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000004779 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
5-methylcytosine rRNA methyltransferase NSUN4D [auth x]384Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000117481 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor 4, mitochondrialE [auth y]381Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122085 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA methyltransferase 2, mitochondrialF [auth z]246Homo sapiensMutation(s): 0 
EC: 2.1.1
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GTEx:  ENSG00000122687 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialG [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialH [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialI [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialJ [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialK [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialL [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialM [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialN [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialO [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialP [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialS [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialT [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialU [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialV [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialW [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialX [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialY [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialZ [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialAA [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialBA [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialCA [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialDA [auth P]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialEA [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialFA [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialGA [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialHA [auth T]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialIA [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialJA [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialKA [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialLA [auth X]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialMA [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialNA [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialOA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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UniProt GroupQ9Y6G3
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialPA [auth b]215Homo sapiensMutation(s): 0 
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PHAROS:  Q8N983
GTEx:  ENSG00000055950 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialQA [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialRA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialSA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialTA [auth f]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialUA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialVA [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialWA [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialXA [auth j]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialYA [auth k]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialZA [auth l]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialAB [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialBB [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialCB [auth p]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1DB [auth q]222Homo sapiensMutation(s): 0 
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Find proteins for Q8TAE8 (Homo sapiens)
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GTEx:  ENSG00000179271 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialEB [auth r]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialFB [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 17
MoleculeChains LengthOrganismImage
16S mitochondrial rRNA, DNA (30-MER),16S mitochondrial rRNAQ [auth A]1,589Homo sapiens
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Entity ID: 18
MoleculeChains LengthOrganismImage
mitochondrial tRNAValR [auth B]72Homo sapiens
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PM8
Query on PM8

Download Ideal Coordinates CCD File 
GB [auth w]S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE
C21 H41 N2 O7 P S
BPRKYNVKIAROET-IBGZPJMESA-N
SAM
Query on SAM

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HB [auth x]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
N
Query on N

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ZE [auth A]ANY 5'-MONOPHOSPHATE NUCLEOTIDE
C5 H11 O7 P
CYZZKTRFOOKUMT-LMVFSUKVSA-N
FES
Query on FES

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DF [auth r]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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IB [auth 0],
JB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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RE [auth A]
SE [auth A]
TE [auth A]
UE [auth A]
VE [auth A]
RE [auth A],
SE [auth A],
TE [auth A],
UE [auth A],
VE [auth A],
WE [auth A],
XE [auth A],
YE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth D]
BC [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth D],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth E],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth O],
DC [auth A],
DD [auth A],
DE [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
SAC
Query on SAC
Y [auth K]L-PEPTIDE LINKINGC5 H9 N O4SER
AYA
Query on AYA
IA [auth U]L-PEPTIDE LINKINGC5 H9 N O3ALA
THC
Query on THC
PA [auth b]L-PEPTIDE LINKINGC6 H11 N O4THR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182341
European Molecular Biology Organization (EMBO)1074-2019
Swiss National Science Foundation182880

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-07-07
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references