7NSI

55S mammalian mitochondrial ribosome with mtRRF (pre) and tRNA(P/E)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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

Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.

Kummer, E.Schubert, K.N.Schoenhut, T.Scaiola, A.Ban, N.

(2021) Mol Cell 81: 2566-2582.e6

  • DOI: 10.1016/j.molcel.2021.03.042
  • Primary Citation of Related Structures:  
    7NQH, 7NQL, 7NSH, 7NSI, 7NSJ

  • PubMed Abstract: 
  • The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail ...

    The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.


    Organizational Affiliation

    Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialA [auth B0]148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialB [auth B1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47C [auth B2]252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
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Entity ID: 4
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39S ribosomal protein L30, mitochondrialD [auth B3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L55E [auth B4]126Sus scrofaMutation(s): 0 
Gene Names: MRPL55
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mF [auth B5]188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
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Entity ID: 7
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39S ribosomal protein L33, mitochondrialG [auth B6]65Sus scrofaMutation(s): 0 
Gene Names: MRPL33
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Entity ID: 9
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39S ribosomal protein L34, mitochondrialI [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L2_C domain-containing proteinJ [auth BD]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ICT1K [auth BE]399Sus scrofaMutation(s): 0 
Gene Names: MRPL3
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Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4L [auth BF]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factor, mitochondrialM [auth BG]257Homo sapiensMutation(s): 0 
Gene Names: MRRF
UniProt & NIH Common Fund Data Resources
Find proteins for Q96E11 (Homo sapiens)
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PHAROS:  Q96E11
GTEx:  ENSG00000148187 
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Entity ID: 14
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39S ribosomal protein L9, mitochondrialN [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 15
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39S ribosomal protein L10, mitochondrial isoform aO [auth BJ]262Sus scrofaMutation(s): 0 
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Entity ID: 16
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39S ribosomal protein L11, mitochondrial isoform aP [auth BK]192Sus scrofaMutation(s): 0 
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Entity ID: 17
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39S ribosomal protein L13, mitochondrialQ [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
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Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
uL14mR [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
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Find proteins for A0A4X1V5Y7 (Sus scrofa)
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Entity ID: 19
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39S ribosomal protein L15, mitochondrialS [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 20
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39S ribosomal protein L16, mitochondrialT [auth BQ]251Sus scrofaMutation(s): 0 
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Entity ID: 21
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39S ribosomal protein L17, mitochondrialU [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
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Entity ID: 22
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39S ribosomal protein L18, mitochondrial isoform 1V [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
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Entity ID: 23
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39S ribosomal protein L19, mitochondrialW [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
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Entity ID: 24
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39S ribosomal protein L20, mitochondrial isoform 1X [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 25
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39S ribosomal protein L21, mitochondrial isoform dY [auth BV]209Sus scrofaMutation(s): 0 
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Entity ID: 26
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39S ribosomal protein L22, mitochondrialZ [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 27
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39S ribosomal protein L23, mitochondrialAA [auth BX]150Sus scrofaMutation(s): 0 
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Entity ID: 28
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39S ribosomal protein L24, mitochondrial isoform X1BA [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 29
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39S ribosomal protein L37, mitochondrialCA [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
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Entity ID: 30
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39S ribosomal protein L38, mitochondrialDA [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
TGS domain-containing proteinEA [auth Bc]334Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L40FA [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Entity ID: 33
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Mitochondrial ribosomal protein L41GA [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 34
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mL42HA [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 35
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39S ribosomal protein L43, mitochondrial isoform X2IA [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 36
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39S ribosomal protein L35, mitochondrialJA [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 37
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39S ribosomal protein L44, mitochondrialKA [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
UniProt
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Entity ID: 38
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Mitochondrial ribosomal protein L45LA [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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39S ribosomal protein L46, mitochondrialMA [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
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Entity ID: 40
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39S ribosomal protein L48, mitochondrialNA [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
UniProt
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Entity ID: 41
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39S ribosomal protein L49, mitochondrialOA [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
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Entity ID: 42
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39S ribosomal protein L50, mitochondrialPA [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
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39S ribosomal protein L51, mitochondrialQA [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 44
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39S ribosomal protein L52, mitochondrialRA [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
mL53SA [auth Bp]112Sus scrofaMutation(s): 0 
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Entity ID: 46
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39S ribosomal protein L54, mitochondrialTA [auth Bq]138Sus scrofaMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57UA [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
UniProt
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L58VA [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
UniProt
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L59, mitochondrialWA [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialXA [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
UniProt
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18AYA [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinAB [auth B9]100Sus scrofaMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialEB [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
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Entity ID: 58
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28S ribosomal protein S24, mitochondrialFB [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
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Entity ID: 59
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28S ribosomal protein S5, mitochondrial isoform X2GB [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
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Entity ID: 60
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Mitochondrial ribosomal protein S6HB [auth AF]276Sus scrofaMutation(s): 0 
Gene Names: MRPS6
UniProt
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Entity ID: 61
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28S ribosomal protein S7, mitochondrialIB [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
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Entity ID: 62
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28S ribosomal protein S9, mitochondrialJB [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
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Entity ID: 63
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28S ribosomal protein S10, mitochondrialKB [auth AJ]200Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S11LB [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
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Entity ID: 65
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Mitoribosomal protein us12m, mrps12MB [auth AL]139Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 66
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28S ribosomal protein S14, mitochondrialNB [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
UniProt
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Entity ID: 67
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28S ribosomal protein S15, mitochondrialOB [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
UniProt
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Entity ID: 68
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28S ribosomal protein S16, mitochondrialPB [auth AP]135Sus scrofaMutation(s): 0 
Gene Names: MRPS16
UniProt
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Entity ID: 69
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uS17mQB [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
UniProt
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Entity ID: 70
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28S ribosomal protein S18c, mitochondrial isoform 1RB [auth AR]143Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 71
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28S ribosomal protein S21, mitochondrialSB [auth AU]87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
UniProt
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
unknownTB [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22UB [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
UniProt
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Entity ID: 74
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Mitochondrial ribosomal protein S23VB [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
UniProt
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Entity ID: 75
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Interferon alpha-inducible protein 6WB [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
UniProt
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Entity ID: 76
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28S ribosomal protein S26, mitochondrialXB [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: MRPS26
UniProt
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27YB [auth Ae]455Sus scrofaMutation(s): 0 
Gene Names: MRPS27
UniProt
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialZB [auth Af]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
UniProt
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
Death associated protein 3AC [auth Ag]410Sus scrofaMutation(s): 0 
Gene Names: DAP3
UniProt
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Entity ID: 80
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28S ribosomal protein S31, mitochondrialBC [auth Ah]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
UniProt
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Entity ID: 81
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Mitochondrial ribosomal protein S33CC [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
UniProt
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Entity ID: 82
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Mitochondrial ribosomal protein S34DC [auth Aj]218Sus scrofaMutation(s): 0 
Gene Names: MRPS34
UniProt
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Entity ID: 83
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28S ribosomal protein S35, mitochondrial isoform 1EC [auth Ak]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
UniProt
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain containing 1FC [auth Am]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
UniProt
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Entity ID: 85
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Aurora kinase A interacting protein 1GC [auth An]199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
UniProt
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Entity ID: 86
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Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,mS39,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3HC [auth Ao]690Sus scrofaMutation(s): 0 
Gene Names: PTCD3
UniProt
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Entity ID: 87
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28S ribosomal protein S18b, mitochondrialIC [auth Ap]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
UniProt
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Entity ID: 88
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
UniProt
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Entity ID: 8
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CP tRNAPheH [auth BB]73Sus scrofa
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