6YDW

55S mammalian mitochondrial ribosome with mtEFG1 and two tRNAMet (TI-POST)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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 insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1.

Kummer, E.Ban, N.

(2020) EMBO J 39: e104820-e104820

  • DOI: https://doi.org/10.15252/embj.2020104820
  • Primary Citation of Related Structures:  
    6YDP, 6YDW

  • PubMed Abstract: 

    Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo-EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase-associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinA [auth AI]397Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19B [auth BT]292Sus scrofaMutation(s): 0 
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Find proteins for I3LNJ0 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20C [auth BU]149Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21D [auth BV]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinE [auth BW]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TXR4 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinF [auth BX]150Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinG [auth BY]216Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37H [auth Ba]423Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BIV6 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38I [auth Bb]380Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RW03 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39J [auth Bc]334Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SHP6 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinK [auth Bd]206Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZP98 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41L [auth Be]135Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1F1K9 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinM [auth Bf]142Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BQA1 (Sus scrofa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43N [auth Bg]159Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S8U4 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinO [auth Bh]332Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45P [auth Bi]306Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46Q [auth Bj]279Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialR [auth Bk]269Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mrpl34S [auth Bl]166Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0R4J8D6 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50T [auth Bm]198Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51U [auth Bn]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1P1C8 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinV [auth Bo]124Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S9B7 (Sus scrofa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mL53W [auth Bp]112Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A341D604 (Neophocaena asiaeorientalis asiaeorientalis)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinX [auth Bq]138Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LN63 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57Y [auth Bt]102Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BP93 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinZ [auth Bu]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinAA [auth Bv]222Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZXA6 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L27BA [auth B0]148Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1U0F6 (Sus scrofa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialCA [auth Bw]433Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480QIM3 (Sus scrofa)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18ADA [auth Bx]196Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2FA [auth AB]289Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1S001 (Sus scrofa)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24GA [auth AC]167Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287ANU4 (Sus scrofa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5HA [auth AE]430Sus scrofaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinIA [auth AF]276Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7JA [auth AG]242Sus scrofaMutation(s): 0 
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Find proteins for A0A286ZJ25 (Sus scrofa)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10KA [auth AJ]200Sus scrofaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mLA [auth AK]196Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12MA [auth AL]139Sus scrofaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14NA [auth AN]128Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mOA [auth AO]239Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287BMP0 (Sus scrofa)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialPA [auth AP]135Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A480JTD7 (Sus scrofa)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mQA [auth AQ]130Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18CRA [auth AR]143Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL54 (Sus scrofa)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mSA [auth AU]87Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZNB3 (Sus scrofa)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptideWA [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22XA [auth Aa]382Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AQT5 (Sus scrofa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mS23YA [auth Ab]190Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25ZA [auth Ac]173Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26AB [auth Ad]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27BB [auth Ae]455Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A5G2R5D6 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28CB [auth B1]256Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mitoribosomal protein ms28, mrps28DB [auth Af]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Death associated protein 3EB [auth Ag]410Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S31FB [auth Ah]387Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
mS33GB [auth Ai]106Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V2H3 (Sus scrofa)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mS34HB [auth Aj]218Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S35IB [auth Ak]325Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mS37JB [auth Am]118Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1KB [auth An]199Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D2A802 (Sus scrofa)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
mS39LB [auth Ao]692Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GKS8 (Sus scrofa)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialMB [auth Ap]258Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47UB [auth B2]252Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinVB [auth B3]161Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1MIP3 (Sus scrofa)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinWB [auth B4]126Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinXB [auth B5]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinYB [auth B6]65Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TLP9 (Sus scrofa)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34ZB [auth B7]95Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35AC [auth B8]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinBC [auth B9]100Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor G, mitochondrialEC [auth BC]721Homo sapiensMutation(s): 0 
Gene Names: GFM1EFGEFG1GFM
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RP9 (Homo sapiens)
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PHAROS:  Q96RP9
GTEx:  ENSG00000168827 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinFC [auth BD]306Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1GC [auth BE]348Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4HC [auth BF]294Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287B9C4 (Sus scrofa)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9IC [auth BI]268Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LR45 (Sus scrofa)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10JC [auth BJ]262Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RWJ0 (Sus scrofa)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11KC [auth BK]192Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RU54 (Sus scrofa)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinLC [auth BN]178Sus scrofaMutation(s): 0 
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinMC [auth BO]145Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinNC [auth BP]296Sus scrofaMutation(s): 0 
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