7NQL

55S mammalian mitochondrial ribosome with ICT1 and P site tRNAMet


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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. 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: eva.kummer@cpr.ku.dk.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34A [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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UniProt GroupA0A4X1UFR4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35B [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinC [auth B9]100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
UniProt
Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mF [auth BD]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
UniProt
Find proteins for F1RRN2 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1G [auth BE]399Sus scrofaMutation(s): 0 
Gene Names: MRPL3
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4H [auth BF]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
UniProt
Find proteins for A0A287B9C4 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9I [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10J [auth BJ]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11K [auth BK]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialL [auth BL]184Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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PHAROS:  Q14197
GTEx:  ENSG00000167862 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mM [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mN [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mO [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mP [auth BQ]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mQ [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18R [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19S [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20T [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21U [auth BV]209Sus scrofaMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mV [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mW [auth BX]150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mX [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37Y [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38Z [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39AA [auth Bc]334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L40BA [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41CA [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL42DA [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43EA [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL44FA [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45GA [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46HA [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialIA [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Mrpl34JA [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50KA [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51LA [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL52MA [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL53NA [auth Bp]112Sus scrofaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL54OA [auth Bq]138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57PA [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)QA [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL64RA [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialSA [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18ATA [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
UniProt
Find proteins for A0A4X1U6S6 (Sus scrofa)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2YA [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
Find proteins for F1S001 (Sus scrofa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24ZA [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
UniProt
Find proteins for A0A287ANU4 (Sus scrofa)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5AB [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
Find proteins for F1SU66 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mBB [auth AF]276Sus scrofaMutation(s): 0 
Gene Names: MRPS6
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7CB [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
Find proteins for A0A286ZJ25 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mDB [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
Find proteins for I3LU08 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10EB [auth AJ]200Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
Find proteins for F1RUU2 (Sus scrofa)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mFB [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
UniProt
Find proteins for A0A286ZJJ6 (Sus scrofa)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12GB [auth AL]139Sus scrofaMutation(s): 0 
Gene Names: MRPS12
UniProt
Find proteins for A0A0M3KL52 (Sus scrofa)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14HB [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
UniProt
Find proteins for A0A0M3KL53 (Sus scrofa)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mIB [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
UniProt
Find proteins for A0A287BMP0 (Sus scrofa)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialJB [auth AP]135Sus scrofaMutation(s): 0 
Gene Names: MRPS16
UniProt
Find proteins for A0A480JTD7 (Sus scrofa)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mKB [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
UniProt
Find proteins for A0A8D1UDM1 (Sus scrofa)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18CMB [auth AR]143Sus scrofaMutation(s): 0 
Gene Names: MRPS18C
UniProt
Find proteins for A0A0M3KL54 (Sus scrofa)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mNB [auth AU]87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
UniProt
Find proteins for A0A286ZNB3 (Sus scrofa)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
unknownQB [auth AZ]18unidentifiedMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22RB [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
UniProt
Find proteins for A0A287AQT5 (Sus scrofa)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
mS23SB [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
UniProt
Find proteins for A0A287AEW3 (Sus scrofa)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25TB [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
UniProt
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26UB [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: MRPS26
UniProt
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27VB [auth Ae]455Sus scrofaMutation(s): 0 
Gene Names: MRPS27
UniProt
Find proteins for A0A5G2R5D6 (Sus scrofa)
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UniProt GroupA0A5G2R5D6
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Mitoribosomal protein ms28, mrps28WB [auth Af]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
UniProt
Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Death associated protein 3XB [auth Ag]410Sus scrofaMutation(s): 0 
Gene Names: DAP3
UniProt
Find proteins for A0A8D1XNL0 (Sus scrofa)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S31YB [auth Ah]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
UniProt
Find proteins for F1RME2 (Sus scrofa)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
mS33ZB [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
UniProt
Find proteins for A0A4X1V2H3 (Sus scrofa)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
mS34AC [auth Aj]218Sus scrofaMutation(s): 0 
Gene Names: MRPS34
UniProt
Find proteins for A0A287AVS9 (Sus scrofa)
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