7NSJ

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

  • Classification: TRANSLATION
  • Organism(s): Sus scrofa
  • Mutation(s): No 

  • Deposited: 2021-03-07 Released: 2021-06-02 
  • Deposition Author(s): Kummer, E., Schubert, K., Ban, N.
  • Funding Organization(s): European Molecular Biology Organization (EMBO), Swiss National Science Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: https://doi.org/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
Mitochondrial ribosomal protein L27A [auth B0]148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28B [auth B1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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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
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mD [auth B3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
bL31mE [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
MoleculeChainsSequence LengthOrganismDetailsImage
bL33mG [auth B6]65Sus scrofaMutation(s): 0 
Gene Names: MRPL33
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34I [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
uL2mJ [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
UniProt
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
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Mitochondrial ribosomal protein L9M [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 14
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Mitochondrial ribosomal protein L10N [auth BJ]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11O [auth BK]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
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Entity ID: 16
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uL13mP [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
uL14mQ [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
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Entity ID: 18
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uL15mR [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 19
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uL16mS [auth BQ]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
bL17mT [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18U [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
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Entity ID: 22
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Mitochondrial ribosomal protein L19V [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
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Entity ID: 23
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Mitochondrial ribosomal protein L20W [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
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Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 24
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Mitochondrial ribosomal protein L21X [auth BV]209Sus scrofaMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
uL22mY [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
uL23mZ [auth BX]150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
uL24mAA [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37BA [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
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Entity ID: 29
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Mitochondrial ribosomal protein L38CA [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
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Entity ID: 30
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Mitochondrial ribosomal protein L39DA [auth Bc]334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
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Entity ID: 31
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Mitochondrial ribosomal protein L40EA [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Find proteins for A0A5G2R2V2 (Sus scrofa)
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Entity ID: 32
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Mitochondrial ribosomal protein L41FA [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 33
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mL42GA [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43HA [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 35
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mL44IA [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
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Entity ID: 36
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Mitochondrial ribosomal protein L35JA [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 37
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Mitochondrial ribosomal protein L45KA [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 38
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Mitochondrial ribosomal protein L46LA [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialMA [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Mrpl34NA [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
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Entity ID: 41
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Mitochondrial ribosomal protein L50OA [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 42
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Mitochondrial ribosomal protein L51PA [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 43
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mL52QA [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 44
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mL53RA [auth Bp]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A341D604 (Neophocaena asiaeorientalis asiaeorientalis)
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Entity ID: 45
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mL54SA [auth Bq]138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 46
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Mitochondrial ribosomal protein L57TA [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
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Entity ID: 47
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mL62 (ICT1)UA [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
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Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
mL64VA [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialWA [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
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Entity ID: 50
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Mitochondrial ribosomal protein S18AXA [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinZA [auth B9]100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
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Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 54
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Mitochondrial ribosomal protein S2BB [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
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Entity ID: 55
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Mitochondrial ribosomal protein S24CB [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
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Entity ID: 56
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28S ribosomal protein S5, mitochondrial isoform X2DB [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
bS6mEB [auth AF]276Sus scrofaMutation(s): 0 
Gene Names: MRPS6
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7FB [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
uS9mGB [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
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Entity ID: 60
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Mitochondrial ribosomal protein S10HB [auth AJ]200Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
uS11mIB [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
UniProt
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12JB [auth AL]139Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 63
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Mitochondrial ribosomal protein S14KB [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
UniProt
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
uS15mLB [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
UniProt
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Entity ID: 65
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28S ribosomal protein S16, mitochondrialMB [auth AP]135Sus scrofaMutation(s): 0 
Gene Names: MRPS16
UniProt
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
uS17mNB [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
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Entity ID: 67
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Mitochondrial ribosomal protein S18COB [auth AR]143Sus scrofaMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
bS21mPB [auth AU]87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
UniProt
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
unknownQB [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22RB [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
mS23SB [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25TB [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
UniProt
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26UB [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: GNRH2
UniProt
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Entity ID: 74
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Mitochondrial ribosomal protein S27VB [auth Ae]455Sus scrofaMutation(s): 0 
Gene Names: MRPS27
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Entity ID: 75
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Mitoribosomal protein ms28, mrps28WB [auth Af]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
UniProt
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
Death associated protein 3XB [auth Ag]410Sus scrofaMutation(s): 0 
Gene Names: DAP3
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialYB [auth Ah]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
UniProt
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
mS33ZB [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
mS34AC [auth Aj]218Sus scrofaMutation(s): 0 
Gene Names: MRPS34
UniProt
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Entity ID: 80
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Mitochondrial ribosomal protein S35BC [auth Ak]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
mS37CC [auth Am]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1DC [auth An]199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,mS39,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3,Pentatricopeptide repeat domain 3EC [auth Ao]690Sus scrofaMutation(s): 0 
Gene Names: PTCD3
UniProt
Find proteins for F1SVC4 (Sus scrofa)
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Entity ID: 84
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28S ribosomal protein S18b, mitochondrialFC [auth Ap]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
UniProt
Find proteins for Q767K8 (Sus scrofa)
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
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Entity ID: 8
MoleculeChainsLengthOrganismImage
CP tRNAPheH [auth BB]73Sus scrofa
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Entity ID: 51
MoleculeChainsLengthOrganismImage
12S rRNAYA [auth AA]962Sus scrofa
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Entity ID: 53
MoleculeChainsLengthOrganismImage
16S rRNAAB [auth BA]1,571Sus scrofa
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Entity ID: 86
MoleculeChainsLengthOrganismImage
tRNA(P/P) and tRNA(E*)MC [auth AV],
OC [auth AY]		71Sus scrofa
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