7L08

Cryo-EM structure of the human 55S mitoribosome-RRFmt complex.

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-12-11 Released: 2021-05-12 
  • Deposition Author(s): Koripella, R., Agrawal, E.K., Deep, A., Agrawal, R.K.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance.

Koripella, R.K.Deep, A.Agrawal, E.K.Keshavan, P.Banavali, N.K.Agrawal, R.K.

(2021) Nat Commun 12: 3607-3607

  • DOI: https://doi.org/10.1038/s41467-021-23726-4
  • Primary Citation of Related Structures:  
    7L08, 7L20

  • PubMed Abstract: 

    Ribosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRF mt ) and a recycling-specific homolog of elongation factor G (EF-G2 mt ). These structures clarify an unusual role of a mitochondria-specific segment of RRF mt , identify the structural distinctions that confer functional specificity to EF-G2 mt , and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2 mt is markedly different from that of mitochondrial elongation factor EF-G1 mt , suggesting that the two human EF-G mt s have evolved diversely to negate the effect of a bacterial antibiotic.


  • Organizational Affiliation

    Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialB [auth AB]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialC [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialD [auth AE]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialE [auth AI]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialF [auth AJ]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialG [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialH [auth AM]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialI [auth AN]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialJ [auth AO]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialK [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialL [auth AQ]87Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000266472 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialM [auth AT]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialN [auth AW]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialO [auth AX]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1P [auth A2]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172586 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialQ [auth AH]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialR [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialS [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialT [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialU [auth AU]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialV [auth AV]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialW [auth AY]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialX [auth AZ]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialY [auth A1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialZ [auth A0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinAA [auth A3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialBA [auth A4]689Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialCA [auth AD]430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialDA [auth AF]242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialEA [auth AG]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialHA [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialIA [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialJA [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialKA [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialLA [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialMA [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialNA [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialOA [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialPA [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialQA [auth T]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialRA [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialSA [auth X]256Homo sapiensMutation(s): 3 
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GTEx:  ENSG00000086504 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialTA [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialUA [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialVA [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialWA [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialXA [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialYA [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialZA [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialAB [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialBB [auth b]155Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialCB [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialDB [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialEB [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAFB [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialGB [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialHB [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1IB [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: 62
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialJB [auth r]196Homo sapiensMutation(s): 0 
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Find proteins for Q9NVS2 (Homo sapiens)
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GTEx:  ENSG00000096080 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialKB [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialLB [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialMB [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18, isoform CRA_bNB [auth P]179Homo sapiensMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialOB [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialPB [auth V]216Homo sapiensMutation(s): 0 
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Find proteins for Q96A35 (Homo sapiens)
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GTEx:  ENSG00000143314 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialQB [auth E]348Homo sapiensMutation(s): 0 
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Find proteins for P09001 (Homo sapiens)
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GTEx:  ENSG00000114686 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialRB [auth 5]423Homo sapiensMutation(s): 0 
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Find proteins for Q9BZE1 (Homo sapiens)
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GTEx:  ENSG00000116221 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialSB [auth 6]380Homo sapiensMutation(s): 0 
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Find proteins for Q96DV4 (Homo sapiens)
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GTEx:  ENSG00000204316 
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