6GAW

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the complete 55S ribosome.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM.

Kummer, E.Leibundgut, M.Rackham, O.Lee, R.G.Boehringer, D.Filipovska, A.Ban, N.

(2018) Nature 560: 263-267

  • DOI: https://doi.org/10.1038/s41586-018-0373-y
  • Primary Citation of Related Structures:  
    6GAW, 6GAZ, 6GB2

  • PubMed Abstract: 

    Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation 1,2 . The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals 3,4 . Furthermore, only one type of methionyl transfer RNA (tRNA Met ) is used for both initiation and elongation 4,5 , necessitating that the initiation factor specifically recognizes the formylated version of tRNA Met (fMet-tRNA Met ). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome 2 . There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA Met and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane.


  • Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12198Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L27G [auth B0]148Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1U0F6 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28H [auth B1]256Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZTW8 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47I [auth B2]252Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mJ [auth B3]161Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1MIP3 (Sus scrofa)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialK [auth B4]126Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mL [auth B5]188Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mM [auth B6]65Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34N [auth B7]95Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35O [auth B8]188Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinP [auth B9]100Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2, mitochondrialS [auth BC]650Homo sapiensMutation(s): 0 
Gene Names: MTIF2
UniProt & NIH Common Fund Data Resources
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PHAROS:  P46199
GTEx:  ENSG00000085760 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialT [auth BD]306Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ICT1U [auth BE]348Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4V [auth BF]294Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9W [auth BI]268Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10X [auth BJ]262Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11Y [auth BK]192Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialAA [auth BN]178Sus scrofaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mBA [auth BO]145Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialCA [auth BP]296Sus scrofaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialDA [auth BQ]251Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialEA [auth BR]169Sus scrofaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18FA [auth BS]180Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19GA [auth BT]292Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L20HA [auth BU]149Sus scrofaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21IA [auth BV]209Sus scrofaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mJA [auth BW]210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mKA [auth BX]150Sus scrofaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialLA [auth BY]216Sus scrofaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37MA [auth Ba]423Sus scrofaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38NA [auth Bb]380Sus scrofaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39OA [auth Bc]334Sus scrofaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrial isoform 1PA [auth Bd]206Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L41QA [auth Be]135Sus scrofaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL42RA [auth Bf]142Sus scrofaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL43SA [auth Bg]159Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialTA [auth Bh]332Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL45UA [auth Bi]306Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L46VA [auth Bj]279Sus scrofaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L48WA [auth Bk]212Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialXA [auth Bl]166Sus scrofaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL50YA [auth Bm]159Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L51ZA [auth Bn]128Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialAB [auth Bo]124Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mL53BB [auth Bp]112Sus scrofaMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL54CB [auth Bq]138Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L57DB [auth Bt]102Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialEB [auth Bu]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZJR2 (Sus scrofa)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mL64FB [auth Bv]222Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mL65GB [auth Bw]433Sus scrofaMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18AHB [auth Bx]196Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
unassigned secondary structure elementsIB [auth Bz]82Sus scrofaMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2KB [auth AB]289Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24LB [auth AC]167Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5MB [auth AE]430Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SU66 (Sus scrofa)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S6NB [auth AF]124Sus scrofaMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7OB [auth AG]242Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A286ZJ25 (Sus scrofa)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialPB [auth AI]397Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LU08 (Sus scrofa)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10QB [auth AJ]201Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialRB [auth AK]196Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12SB [auth AL]139Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL52 (Sus scrofa)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14TB [auth AN]128Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL53 (Sus scrofa)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinUB [auth AO]239Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mVB [auth AP]135Sus scrofaMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mWB [auth AQ]130Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1UDM1 (Sus scrofa)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18CXB [auth AR]143Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL54 (Sus scrofa)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mYB [auth AU]87Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
unassigned secondary structure elementsBC [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S22CC [auth Aa]382Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AQT5 (Sus scrofa)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialDC [auth Ab]190Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25EC [auth Ac]173Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL55 (Sus scrofa)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S26FC [auth Ad]205Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AY01 (Sus scrofa)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
mS27GC [auth Ae]455Sus scrofaMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialHC [auth Af]188Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A0M3KL56 (Sus scrofa)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Death associated protein 3IC [auth Ag]397Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1XNL0 (Sus scrofa)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
mS31JC [auth Ah]387Sus scrofaMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
mS33KC [auth Ai]106Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1V2H3 (Sus scrofa)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialLC [auth Aj]218Sus scrofaMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialMC [auth Ak]325Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1SG95 (Sus scrofa)
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1NC [auth Am]118Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1SZV4 (Sus scrofa)
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1OC [auth An]199Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D2A802 (Sus scrofa)
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