8OIR

55S human mitochondrial ribosome with mtRF1 and P-site tRNA


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

Molecular basis of translation termination at noncanonical stop codons in human mitochondria.

Saurer, M.Leibundgut, M.Nadimpalli, H.P.Scaiola, A.Schonhut, T.Lee, R.G.Siira, S.J.Rackham, O.Dreos, R.Lenarcic, T.Kummer, E.Gatfield, D.Filipovska, A.Ban, N.

(2023) Science 380: 531-536

  • DOI: https://doi.org/10.1126/science.adf9890
  • Primary Citation of Related Structures:  
    8OIN, 8OIP, 8OIQ, 8OIR, 8OIS, 8OIT

  • PubMed Abstract: 

    The genetic code that specifies the identity of amino acids incorporated into proteins during protein synthesis is almost universally conserved. Mitochondrial genomes feature deviations from the standard genetic code, including the reassignment of two arginine codons to stop codons. The protein required for translation termination at these noncanonical stop codons to release the newly synthesized polypeptides is not currently known. In this study, we used gene editing and ribosomal profiling in combination with cryo-electron microscopy to establish that mitochondrial release factor 1 (mtRF1) detects noncanonical stop codons in human mitochondria by a previously unknown mechanism of codon recognition. We discovered that binding of mtRF1 to the decoding center of the ribosome stabilizes a highly unusual conformation in the messenger RNA in which the ribosomal RNA participates in specific recognition of the noncanonical stop codons.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrial198Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000262814 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialJ [auth BA]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialK [auth BB]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialL [auth BC]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialM [auth BD]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialN [auth BE]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialO [auth BF]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialP [auth BG]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialQ [auth BH]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialR [auth BI]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialS [auth BJ]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialT [auth BK]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialU [auth BL]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialV [auth BM]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialW [auth BN]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialX [auth BO]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialY [auth BP]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialZ [auth BQ]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialAA [auth BR]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialBA [auth BS]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialCA [auth BT]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialDA [auth BU]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialEA [auth BV]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialFA [auth BW]180Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112110 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialGA [auth BX]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialHA [auth BY]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialIA [auth BZ]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialJA [auth Ba]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172590 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialKA [auth Bb]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialLA [auth Bc]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialMA [auth Bd]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialNA [auth Be]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialOA [auth Bf]206Homo sapiensMutation(s): 0 
EC: 3.1.1.29
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GTEx:  ENSG00000167862 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1PA [auth Bg]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialQA [auth Bh]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialRA [auth Bi]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L1, mitochondrialSA [auth Bj]325Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169288 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialTA [auth Bl]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialUA [auth Bm]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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UniProt GroupQ9BZE1
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialVA [auth Bn]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialWA [auth Bo]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialXA [auth Bp]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialYA [auth Bq]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialZA [auth Br]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialAB [auth Bs]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialBB [auth Bt]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialCB [auth Bu]306Homo sapiensMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialDB [auth Bv]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialEB [auth Bw]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialFB [auth Bx]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialGB [auth By]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialHB [auth Bz]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialJB [auth AB]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialKB [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinLB [auth AD]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialMB [auth AE]125Homo sapiensMutation(s): 0 
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Find proteins for P82932 (Homo sapiens)
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GTEx:  ENSG00000243927 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialNB [auth AF]242Homo sapiensMutation(s): 0 
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Find proteins for Q9Y2R9 (Homo sapiens)
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GTEx:  ENSG00000125445 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialPB [auth AH]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialRB [auth AJ]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialSB [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialTB [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialUB [auth AM]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialVB [auth AN]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialWB [auth AO]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialXB [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialYB [auth AQ]87Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000266472 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialZB [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialAC [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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