6ZS9

Human mitochondrial ribosome in complex with ribosome recycling factor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 4.1 of the entry. See complete history


Literature

Structural basis of mitochondrial translation.

Aibara, S.Singh, V.Modelska, A.Amunts, A.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58362
  • Primary Citation of Related Structures:  
    6ZS9, 6ZSA, 6ZSB, 6ZSC, 6ZSD, 6ZSE, 6ZSG, 7OG4

  • PubMed Abstract: 

    Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 Å resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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UniProt GroupQ9BYC8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialD [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialE [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialF [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialG [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialH [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialI [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialJ [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialL [auth A0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialM [auth A1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1N [auth A2]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172586 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinO [auth A3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialP [auth A4]634Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factor, mitochondrialQ [auth A5]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148187 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialS [auth AB]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialT [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialU [auth AD]430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialV [auth AE]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialW [auth AF]242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialX [auth AG]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialY [auth AH]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialZ [auth AI]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialAA [auth AJ]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialBA [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialCA [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialDA [auth AM]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialEA [auth AN]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialFA [auth AO]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialGA [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialHA [auth AQ]86Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000266472 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialIA [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialJA [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialKA [auth AT]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialLA [auth AU]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialMA [auth AV]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialNA [auth AW]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialOA [auth AX]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialPA [auth AY]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialQA [auth AZ]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialSA [auth XD]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialTA [auth XE]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialUA [auth XF]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialVA [auth XH]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialWA [auth XI]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialXA [auth XJ]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialYA [auth XK]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialZA [auth XL]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialAB [auth XM]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialBB [auth XN]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialCB [auth XO]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18, isoform CRA_bDB [auth XP]179Homo sapiensMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialEB [auth XQ]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialFB [auth XR]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialGB [auth XS]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialHB [auth XT]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialIB [auth XU]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialJB [auth XV]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialKB [auth XW]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialLB [auth XX]256Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000086504 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialMB [auth XY]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialNB [auth XZ]161Homo sapiensMutation(s): 0 
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Find proteins for Q8TCC3 (Homo sapiens)
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GTEx:  ENSG00000185414 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialOB [auth a]142Homo sapiensMutation(s): 0 
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Find proteins for Q9Y6G3 (Homo sapiens)
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GTEx:  ENSG00000198015 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialPB [auth b]215Homo sapiensMutation(s): 0 
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Find proteins for Q8N983 (Homo sapiens)
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GTEx:  ENSG00000055950 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialQB [auth c]332Homo sapiensMutation(s): 0 
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialRB [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialSB [auth e]279Homo sapiensMutation(s): 0 
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