6YDP

55S mammalian mitochondrial ribosome with mtEFG1 and P site fMet-tRNAMet (POST)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
Mitochondrial ribosomal protein L27A [auth B0]148Sus scrofaMutation(s): 0 
Gene Names: MRPL27
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20B [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21C [auth BV]209Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RY70 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mD [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mE [auth BX]150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mF [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
UniProt
Find proteins for F1RHJ1 (Sus scrofa)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37G [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
UniProt
Find proteins for A0A287BIV6 (Sus scrofa)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38H [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
UniProt
Find proteins for F1RW03 (Sus scrofa)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39I [auth Bc]334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
UniProt
Find proteins for F1SHP6 (Sus scrofa)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinJ [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
UniProt
Find proteins for A0A286ZP98 (Sus scrofa)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41K [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
mL42L [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
UniProt
Find proteins for A0A287BQA1 (Sus scrofa)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L43M [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
UniProt
Find proteins for F1S8U4 (Sus scrofa)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
mL44N [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
UniProt
Find proteins for F1SR64 (Sus scrofa)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L45O [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46P [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
UniProt
Find proteins for F1SRT0 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialQ [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
UniProt
Find proteins for A0A480J9Z6 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mrpl34R [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
UniProt
Find proteins for A0A0R4J8D6 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L50S [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
UniProt
Find proteins for I3L9H6 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51T [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mL52U [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
UniProt
Find proteins for F1S9B7 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mL53V [auth Bp]112Sus scrofaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mL54W [auth Bq]138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
UniProt
Find proteins for I3LN63 (Sus scrofa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57X [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
UniProt
Find proteins for A0A287BP93 (Sus scrofa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)Y [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
UniProt
Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
mL64Z [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
UniProt
Find proteins for A0A286ZXA6 (Sus scrofa)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialAA [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
UniProt
Find proteins for A0A480QIM3 (Sus scrofa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28BA [auth B1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18ACA [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2EA [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24FA [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
UniProt
Find proteins for A0A287ANU4 (Sus scrofa)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5GA [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
Find proteins for F1SU66 (Sus scrofa)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mHA [auth AF]276Sus scrofaMutation(s): 0 
Gene Names: MRPS6
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7IA [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mJA [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10KA [auth AJ]200Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mLA [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
UniProt
Find proteins for A0A286ZJJ6 (Sus scrofa)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12MA [auth AL]139Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL52 (Sus scrofa)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14NA [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mOA [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
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 
Gene Names: MRPS16
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mQA [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
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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 
Gene Names: MRPS21
UniProt
Find proteins for A0A286ZNB3 (Sus scrofa)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
unknown peptideVA [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22WA [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
UniProt
Find proteins for A0A287AQT5 (Sus scrofa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mS23XA [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
UniProt
Find proteins for A0A287AEW3 (Sus scrofa)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25YA [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
UniProt
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26ZA [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: GNRH2
UniProt
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27AB [auth Ae]426Sus scrofaMutation(s): 0 
Gene Names: MRPS27
UniProt
Find proteins for I3LK09 (Sus scrofa)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitoribosomal protein ms28, mrps28BB [auth Af]188Sus scrofaMutation(s): 0 
Gene Names: MRPS28
UniProt
Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47CB [auth B2]252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
UniProt
Find proteins for F1SGC7 (Sus scrofa)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Death associated protein 3DB [auth Ag]410Sus scrofaMutation(s): 0 
Gene Names: DAP3
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S31EB [auth Ah]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
UniProt
Find proteins for F1RME2 (Sus scrofa)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
mS33FB [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mS34GB [auth Aj]218Sus scrofaMutation(s): 0 
Gene Names: MRPS34
UniProt
Find proteins for A0A287AVS9 (Sus scrofa)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S35HB [auth Ak]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
UniProt
Find proteins for F1SG95 (Sus scrofa)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mS37IB [auth Am]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1JB [auth An]199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain 3KB [auth Ao]699Sus scrofaMutation(s): 0 
Gene Names: PTCD3
UniProt
Find proteins for K7GKS8 (Sus scrofa)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialLB [auth Ap]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
UniProt
Find proteins for Q767K8 (Sus scrofa)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mTB [auth B3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mUB [auth B4]126Sus scrofaMutation(s): 0 
Gene Names: MRPL55
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mVB [auth B5]188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
UniProt
Find proteins for I3LTC4 (Sus scrofa)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mWB [auth B6]65Sus scrofaMutation(s): 0 
Gene Names: MRPL33
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34XB [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35YB [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
UniProt
Find proteins for F1SVC5 (Sus scrofa)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinZB [auth B9]100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
UniProt
Find proteins for A0A287A731 (Sus scrofa)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor G, mitochondrialCC [auth BC]722Homo sapiensMutation(s): 0 
Gene Names: GFM1EFGEFG1GFM
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RP9 (Homo sapiens)
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PHAROS:  Q96RP9
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mDC [auth BD]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
UniProt
Find proteins for F1RRN2 (Sus scrofa)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1EC [auth BE]348Sus scrofaMutation(s): 0 
Gene Names: MRPL3
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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UniProt GroupA0A140UHW4
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4FC [auth BF]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
UniProt
Find proteins for A0A287B9C4 (Sus scrofa)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9GC [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
UniProt
Find proteins for I3LR45 (Sus scrofa)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10HC [auth BJ]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
UniProt
Find proteins for F1RWJ0 (Sus scrofa)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11IC [auth BK]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
UniProt
Find proteins for F1RU54 (Sus scrofa)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mJC [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
UniProt
Find proteins for K7GP19 (Sus scrofa)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mKC [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
UniProt
Find proteins for A0A287BMZ6 (Sus scrofa)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mLC [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mMC [auth BQ]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
UniProt
Find proteins for F1RI89 (Sus scrofa)
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinNC [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
UniProt
Find proteins for F1RMQ4 (Sus scrofa)
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18OC [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
UniProt
Find proteins for A0A286ZNK1 (Sus scrofa)
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19PC [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
UniProt
Find proteins for I3LNJ0 (Sus scrofa)
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UniProt GroupI3LNJ0
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