6VLZ

Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI)

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-01-27 Released: 2020-08-05 
  • Deposition Author(s): Sharma, M.R., Koripella, R.K., Agrawal, R.K.
  • Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 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

Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation.

Koripella, R.K., Sharma, M.R., Bhargava, K., Datta, P.P., Kaushal, P.S., Keshavan, P., Spremulli, L.L., Banavali, N.K., Agrawal, R.K.

(2020) Nat Commun 11: 3830-3830

  • DOI: https://doi.org/10.1038/s41467-020-17715-2
  • Primary Citation of Related Structures:  
    6VLZ, 6VMI

  • PubMed Abstract: 

    The mammalian mitochondrial ribosome (mitoribosome) and its associated translational factors have evolved to accommodate greater participation of proteins in mitochondrial translation. Here we present the 2.68-3.96 Å cryo-EM structures of the human 55S mitoribosome in complex with the human mitochondrial elongation factor G1 (EF-G1 mt ) in three distinct conformational states, including an intermediate state and a post-translocational state. These structures reveal the role of several mitochondria-specific (mito-specific) mitoribosomal proteins (MRPs) and a mito-specific segment of EF-G1 mt in mitochondrial tRNA (tRNA mt ) translocation. In particular, the mito-specific C-terminal extension in EF-G1 mt is directly involved in translocation of the acceptor arm of the A-site tRNA mt . In addition to the ratchet-like and independent head-swiveling motions exhibited by the small mitoribosomal subunit, we discover significant conformational changes in MRP mL45 at the nascent polypeptide-exit site within the large mitoribosomal subunit that could be critical for tethering of the elongating mitoribosome onto the inner-mitochondrial membrane.

    • Organizational Affiliation: 

    Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialB [auth AB]296Homo sapiensMutation(s): 0 
Gene Names: MRPS2, CGI-91
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialC [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24, HSPC335
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Find proteins for Q96EL2 (Homo sapiens)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialD [auth AE]125Homo sapiensMutation(s): 0 
Gene Names: MRPS6, C21orf101, RPMS6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialE [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11, RPMS11, HCC2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialF [auth AJ]138Homo sapiensMutation(s): 0 
Gene Names: MRPS12, RPMS12, RPSM12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialG [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialH [auth AM]137Homo sapiensMutation(s): 0 
Gene Names: MRPS16, RPMS16, CGI-132
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialI [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17, RPMS17, HSPC011
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialJ [auth AO]258Homo sapiensMutation(s): 0 
Gene Names: MRPS18B, C6orf14, HSPC183, PTD017
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialK [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18C, CGI-134
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialL [auth AQ]87Homo sapiensMutation(s): 0 
Gene Names: MRPS21, RPMS21, MDS016
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialM [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25, RPMS25
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialN [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28, MRPS35, HSPC007
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialO [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3, MRPS29
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1P [auth A2]118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1, C10orf34, MRPS37
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialQ [auth AH]201Homo sapiensMutation(s): 0 
Gene Names: MRPS10, MSTP040
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialR [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15, RPMS15, DC37
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialS [auth AR]360Homo sapiensMutation(s): 0 
Gene Names: MRPS22, C3orf5, RPMS22, GK002
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialT [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23, CGI-138, HSPC329
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialU [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26, C20orf193, RPMS13
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialV [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27, KIAA0264
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialW [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31, IMOGN38
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialX [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33, CGI-139, PTD003
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialY [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35, MRPS28, HDCMD11P, MDS023, PSEC0213
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialZ [auth A0]218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinAA [auth A3]199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1, AIP, AKIP, MRPS38
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialBA [auth A4]689Homo sapiensMutation(s): 0 
Gene Names: PTCD3, MRPS39, TRG15
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialCA [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialDA [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialEA [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9, RPMS9
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialHA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialIA [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialJA [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialKA [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialLA [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialMA [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialNA [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialOA [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialPA [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialQA [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialRA [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialSA [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28, MAAT1
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialTA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialUA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialVA [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialWA [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialXA [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialYA [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialZA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialAB [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialBB [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialCB [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialDB [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialEB [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAFB [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialGB [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialHB [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1IB [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialJB [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialKB [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialLB [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialMB [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein L18, isoform CRA_bNB [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18, hCG_34030
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialOB [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialPB [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialQB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialRB [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialSB [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialTB [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialUB [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialVB [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialWB [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialXB [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialYB [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialZB [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialAC [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialBC [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialCC [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
UniProt & NIH Common Fund Data Resources
Find proteins for Q14197 (Homo sapiens)
Explore Q14197 
Go to UniProtKB:  Q14197
PHAROS:  Q14197