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: 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 ...

    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
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 L20B [auth BU]149Sus scrofaMutation(s): 0 
Gene Names: MRPL20
UniProt
Find proteins for A0A286ZU56 (Sus scrofa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L21C [auth BV]209Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
uL22mD [auth BW]210Sus scrofaMutation(s): 0 
Gene Names: MRPL22
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
uL23mE [auth BX]150Sus scrofaMutation(s): 0 
Gene Names: MRPL23
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
uL24mF [auth BY]216Sus scrofaMutation(s): 0 
Gene Names: MRPL24
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L37G [auth Ba]423Sus scrofaMutation(s): 0 
Gene Names: MRPL37
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L38H [auth Bb]380Sus scrofaMutation(s): 0 
Gene Names: MRPL38
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L39I [auth Bc]334Sus scrofaMutation(s): 0 
Gene Names: MRPL39
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinJ [auth Bd]206Sus scrofaMutation(s): 0 
Gene Names: MRPL40
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Entity ID: 11
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Mitochondrial ribosomal protein L41K [auth Be]135Sus scrofaMutation(s): 0 
Gene Names: MRPL41
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
mL42L [auth Bf]142Sus scrofaMutation(s): 0 
Gene Names: MRPL42
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Entity ID: 13
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Mitochondrial ribosomal protein L43M [auth Bg]159Sus scrofaMutation(s): 0 
Gene Names: MRPL43
UniProt
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Entity ID: 14
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mL44N [auth Bh]332Sus scrofaMutation(s): 0 
Gene Names: MRPL44
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Entity ID: 15
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Mitochondrial ribosomal protein L45O [auth Bi]306Sus scrofaMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 16
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Mitochondrial ribosomal protein L46P [auth Bj]279Sus scrofaMutation(s): 0 
Gene Names: MRPL46
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Entity ID: 17
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39S ribosomal protein L48, mitochondrialQ [auth Bk]269Sus scrofaMutation(s): 0 
Gene Names: MRPL48
UniProt
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Entity ID: 18
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Mrpl34R [auth Bl]166Sus scrofaMutation(s): 0 
Gene Names: MRPL49
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Entity ID: 19
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Mitochondrial ribosomal protein L50S [auth Bm]198Sus scrofaMutation(s): 0 
Gene Names: MRPL50
UniProt
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Entity ID: 20
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Mitochondrial ribosomal protein L51T [auth Bn]128Sus scrofaMutation(s): 0 
Gene Names: MRPL51
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
mL52U [auth Bo]124Sus scrofaMutation(s): 0 
Gene Names: MRPL52
UniProt
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Entity ID: 22
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mL53V [auth Bp]112Sus scrofaMutation(s): 0 
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Entity ID: 23
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mL54W [auth Bq]138Sus scrofaMutation(s): 0 
Gene Names: MRPL54
UniProt
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Entity ID: 24
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Mitochondrial ribosomal protein L57X [auth Bt]102Sus scrofaMutation(s): 0 
Gene Names: MRPL57
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
mL62 (ICT1)Y [auth Bu]205Sus scrofaMutation(s): 0 
Gene Names: MRPL58
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
mL64Z [auth Bv]222Sus scrofaMutation(s): 0 
Gene Names: GADD45GIP1
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialAA [auth Bw]433Sus scrofaMutation(s): 0 
Gene Names: MRPS30
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L28BA [auth B1]256Sus scrofaMutation(s): 0 
Gene Names: MRPL28
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18ACA [auth Bx]196Sus scrofaMutation(s): 0 
Gene Names: MRPS18A
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S2EA [auth AB]289Sus scrofaMutation(s): 0 
Gene Names: MRPS2
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S24FA [auth AC]167Sus scrofaMutation(s): 0 
Gene Names: MRPS24
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S5GA [auth AE]430Sus scrofaMutation(s): 0 
Gene Names: MRPS5
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
bS6mHA [auth AF]276Sus scrofaMutation(s): 0 
Gene Names: MRPS6
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S7IA [auth AG]242Sus scrofaMutation(s): 0 
Gene Names: MRPS7
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
uS9mJA [auth AI]397Sus scrofaMutation(s): 0 
Gene Names: MRPS9
UniProt
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S10KA [auth AJ]200Sus scrofaMutation(s): 0 
Gene Names: MRPS10
UniProt
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
uS11mLA [auth AK]196Sus scrofaMutation(s): 0 
Gene Names: MRPS11
UniProt
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S12MA [auth AL]139Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S14NA [auth AN]128Sus scrofaMutation(s): 0 
Gene Names: MRPS14
UniProt
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
uS15mOA [auth AO]239Sus scrofaMutation(s): 0 
Gene Names: MRPS15
UniProt
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialPA [auth AP]135Sus scrofaMutation(s): 0 
Gene Names: MRPS16
UniProt
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
uS17mQA [auth AQ]130Sus scrofaMutation(s): 0 
Gene Names: MRPS17
UniProt
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Entity ID: 44
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Mitochondrial ribosomal protein S18CRA [auth AR]143Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
bS21mSA [auth AU]87Sus scrofaMutation(s): 0 
Gene Names: MRPS21
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
unknown peptideVA [auth AZ]18Sus scrofaMutation(s): 0 
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Entity ID: 49
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Mitochondrial ribosomal protein S22WA [auth Aa]382Sus scrofaMutation(s): 0 
Gene Names: MRPS22
UniProt
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
mS23XA [auth Ab]190Sus scrofaMutation(s): 0 
Gene Names: MRPS23
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S25YA [auth Ac]173Sus scrofaMutation(s): 0 
Gene Names: MRPS25
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Entity ID: 52
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Mitochondrial ribosomal protein S26ZA [auth Ad]205Sus scrofaMutation(s): 0 
Gene Names: GNRH2
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S27AB [auth Ae]426Sus scrofaMutation(s): 0 
Gene Names: MRPS27
UniProt
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Entity ID: 54
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L47CB [auth B2]252Sus scrofaMutation(s): 0 
Gene Names: MRPL47
UniProt
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Death associated protein 3DB [auth Ag]410Sus scrofaMutation(s): 0 
Gene Names: DAP3
UniProt
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Entity ID: 57
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Mitochondrial ribosomal protein S31EB [auth Ah]387Sus scrofaMutation(s): 0 
Gene Names: MRPS31
UniProt
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
mS33FB [auth Ai]106Sus scrofaMutation(s): 0 
Gene Names: MRPS33
UniProt
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Entity ID: 59
MoleculeChainsSequence 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
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S35HB [auth Ak]325Sus scrofaMutation(s): 0 
Gene Names: MRPS35
UniProt
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
mS37IB [auth Am]118Sus scrofaMutation(s): 0 
Gene Names: CHCHD1
UniProt
Find proteins for F1SU49 (Sus scrofa)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A interacting protein 1JB [auth An]199Sus scrofaMutation(s): 0 
Gene Names: AURKAIP1
UniProt
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain 3KB [auth Ao]699Sus scrofaMutation(s): 0 
Gene Names: PTCD3
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialLB [auth Ap]258Sus scrofaMutation(s): 0 
Gene Names: MRPS18B
UniProt
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L12MB [auth CL], NB [auth DL], OB [auth EL], PB [auth FL], QB [auth GL], RB [auth HL], SB [auth LL]198Sus scrofaMutation(s): 0 
Gene Names: MRPL12
UniProt
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mTB [auth B3]161Sus scrofaMutation(s): 0 
Gene Names: MRPL30
UniProt
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
bL31mUB [auth B4]126Sus scrofaMutation(s): 0 
Gene Names: MRPL55
UniProt
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mVB [auth B5]188Sus scrofaMutation(s): 0 
Gene Names: MRPL32
UniProt
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
bL33mWB [auth B6]65Sus scrofaMutation(s): 0 
Gene Names: MRPL33
UniProt
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L34XB [auth B7]95Sus scrofaMutation(s): 0 
Gene Names: MRPL34
UniProt
Find proteins for A0A287A119 (Sus scrofa)
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L35YB [auth B8]188Sus scrofaMutation(s): 0 
Gene Names: MRPL35
UniProt
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal proteinZB [auth B9]100Sus scrofaMutation(s): 0 
Gene Names: MRPL36
UniProt
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor G, mitochondrialCC [auth BC]722Homo sapiensMutation(s): 0 
Gene Names: GFM1EFGEFG1GFM
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PHAROS:  Q96RP9
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
uL2mDC [auth BD]306Sus scrofaMutation(s): 0 
Gene Names: MRPL2
UniProt
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
ICT1EC [auth BE]348Sus scrofaMutation(s): 0 
Gene Names: MRPL3
UniProt
Find proteins for A0A140UHW4 (Sus scrofa)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L4FC [auth BF]294Sus scrofaMutation(s): 0 
Gene Names: MRPL4
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L9GC [auth BI]268Sus scrofaMutation(s): 0 
Gene Names: MRPL9
UniProt
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L10HC [auth BJ]262Sus scrofaMutation(s): 0 
Gene Names: MRPL10
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L11IC [auth BK]192Sus scrofaMutation(s): 0 
Gene Names: MRPL11
UniProt
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
uL13mJC [auth BN]178Sus scrofaMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
uL14mKC [auth BO]145Sus scrofaMutation(s): 0 
Gene Names: MRPL14
UniProt
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
uL15mLC [auth BP]296Sus scrofaMutation(s): 0 
Gene Names: MRPL15
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
uL16mMC [auth BQ]251Sus scrofaMutation(s): 0 
Gene Names: MRPL16
UniProt
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinNC [auth BR]169Sus scrofaMutation(s): 0 
Gene Names: MRPL17
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18OC [auth BS]180Sus scrofaMutation(s): 0 
Gene Names: MRPL18
UniProt
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L19PC [auth BT]292Sus scrofaMutation(s): 0 
Gene Names: MRPL19
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Entity ID: 30
MoleculeChainsLengthOrganismImage
12S rRNADA [auth AA], AC [auth BA]16770Sus scrofa
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Entity ID: 46
MoleculeChainsLengthOrganismImage
fMet-tRNAMet (P site)TA [auth AV]71Homo sapiens
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  • Entity ID: 47
    MoleculeChainsLengthOrganismImage
    mRNAUA [auth AX]6Homo sapiens
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    Entity ID: 73
    MoleculeChainsLengthOrganismImage
    CP tRNAPheBC [auth BB]73Sus scrofa
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    Small Molecules
    Ligands 7 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GTP (Subject of Investigation/LOI)
    Query on GTP

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    ZG [auth Ag]GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    GNP (Subject of Investigation/LOI)
    Query on GNP

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    JP [auth BC]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    5GP (Subject of Investigation/LOI)
    Query on 5GP

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    EP [auth BA], FP [auth BA]GUANOSINE-5'-MONOPHOSPHATE
    C10 H14 N5 O8 P
    RQFCJASXJCIDSX-UUOKFMHZSA-N
     Ligand Interaction
    SPM (Subject of Investigation/LOI)
    Query on SPM

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    GP [auth BA], HP [auth BA], VC [auth AA]SPERMINE
    C10 H26 N4
    PFNFFQXMRSDOHW-UHFFFAOYSA-N
     Ligand Interaction
    FME (Subject of Investigation/LOI)
    Query on FME

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    WG [auth AV]N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    DH [auth Ap], FH [auth B5], GH [auth B9], UC [auth Bx], VG [auth AR], YG [auth Ac]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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