6VMI

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

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2020-01-28 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: 2.96 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: 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 ...

    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 Biomedical Sciences, University at Albany, SUNY, Albany, NY, 12201-0509, USA. rajendra.agrawal@health.ny.gov.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialB [auth AB]296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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GTEx:  ENSG00000122140 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialC [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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GTEx:  ENSG00000062582 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialD [auth AE]125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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GTEx:  ENSG00000243927 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialE [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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GTEx:  ENSG00000181991 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialF [auth AJ]138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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GTEx:  ENSG00000128626 
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Entity ID: 7
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28S ribosomal protein S14, mitochondrialG [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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GTEx:  ENSG00000120333 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialH [auth AM]137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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GTEx:  ENSG00000182180 
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Entity ID: 9
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28S ribosomal protein S17, mitochondrialI [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialJ [auth AO]258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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GTEx:  ENSG00000204568 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialK [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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GTEx:  ENSG00000163319 
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Entity ID: 12
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28S ribosomal protein S21, mitochondrialL [auth AQ]87Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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GTEx:  ENSG00000266472 
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Entity ID: 13
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28S ribosomal protein S25, mitochondrialM [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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GTEx:  ENSG00000131368 
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Entity ID: 14
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28S ribosomal protein S28, mitochondrialN [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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GTEx:  ENSG00000147586 
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Entity ID: 15
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28S ribosomal protein S29, mitochondrialO [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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GTEx:  ENSG00000132676 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1P [auth A2]118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
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GTEx:  ENSG00000172586 
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Entity ID: 17
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28S ribosomal protein S10, mitochondrialQ [auth AH]201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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GTEx:  ENSG00000048544 
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Entity ID: 18
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28S ribosomal protein S15, mitochondrialR [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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GTEx:  ENSG00000116898 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialS [auth AR]360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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GTEx:  ENSG00000175110 
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Entity ID: 20
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28S ribosomal protein S23, mitochondrialT [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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GTEx:  ENSG00000181610 
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Entity ID: 21
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28S ribosomal protein S26, mitochondrialU [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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GTEx:  ENSG00000125901 
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Entity ID: 22
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28S ribosomal protein S27, mitochondrialV [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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GTEx:  ENSG00000113048 
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Entity ID: 23
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28S ribosomal protein S31, mitochondrialW [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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GTEx:  ENSG00000102738 
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Entity ID: 24
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28S ribosomal protein S33, mitochondrialX [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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GTEx:  ENSG00000090263 
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Entity ID: 25
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28S ribosomal protein S35, mitochondrialY [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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GTEx:  ENSG00000061794 
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Entity ID: 26
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28S ribosomal protein S34, mitochondrialZ [auth A0]218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinAA [auth A3]199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
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GTEx:  ENSG00000175756 
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Entity ID: 28
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Pentatricopeptide repeat domain-containing protein 3, mitochondrialBA [auth A4]689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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GTEx:  ENSG00000132300 
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Entity ID: 29
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28S ribosomal protein S5, mitochondrialCA [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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GTEx:  ENSG00000144029 
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Entity ID: 30
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28S ribosomal protein S7, mitochondrialDA [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 31
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28S ribosomal protein S9, mitochondrialEA [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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GTEx:  ENSG00000135972 
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Entity ID: 34
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39S ribosomal protein L2, mitochondrialHA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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GTEx:  ENSG00000112651 
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Entity ID: 35
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39S ribosomal protein L4, mitochondrialIA [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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GTEx:  ENSG00000105364 
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Entity ID: 36
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39S ribosomal protein L9, mitochondrialJA [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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GTEx:  ENSG00000143436 
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Entity ID: 37
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39S ribosomal protein L13, mitochondrialKA [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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GTEx:  ENSG00000172172 
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Entity ID: 38
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39S ribosomal protein L14, mitochondrialLA [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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GTEx:  ENSG00000180992 
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Entity ID: 39
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39S ribosomal protein L15, mitochondrialMA [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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GTEx:  ENSG00000137547 
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Entity ID: 40
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39S ribosomal protein L17, mitochondrialNA [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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GTEx:  ENSG00000158042 
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Entity ID: 41
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39S ribosomal protein L20, mitochondrialOA [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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GTEx:  ENSG00000242485 
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Entity ID: 42
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39S ribosomal protein L21, mitochondrialPA [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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GTEx:  ENSG00000197345 
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Entity ID: 43
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39S ribosomal protein L22, mitochondrialQA [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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GTEx:  ENSG00000082515 
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Entity ID: 44
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39S ribosomal protein L27, mitochondrialRA [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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GTEx:  ENSG00000108826 
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Entity ID: 45
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39S ribosomal protein L28, mitochondrialSA [auth X]256Homo sapiensMutation(s): 3 
Gene Names: MRPL28MAAT1
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GTEx:  ENSG00000086504 
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Entity ID: 46
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39S ribosomal protein L47, mitochondrialTA [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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GTEx:  ENSG00000136522 
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Entity ID: 47
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39S ribosomal protein L30, mitochondrialUA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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GTEx:  ENSG00000185414 
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Entity ID: 48
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39S ribosomal protein L32, mitochondrialVA [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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GTEx:  ENSG00000106591 
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Entity ID: 49
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39S ribosomal protein L33, mitochondrialWA [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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GTEx:  ENSG00000243147 
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Entity ID: 50
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39S ribosomal protein L34, mitochondrialXA [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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GTEx:  ENSG00000130312 
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Entity ID: 51
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39S ribosomal protein L35, mitochondrialYA [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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GTEx:  ENSG00000132313 
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Entity ID: 52
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39S ribosomal protein L36, mitochondrialZA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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GTEx:  ENSG00000171421 
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Entity ID: 53
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39S ribosomal protein L40, mitochondrialAB [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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GTEx:  ENSG00000185608 
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Entity ID: 54
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39S ribosomal protein L43, mitochondrialBB [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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GTEx:  ENSG00000055950 
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Entity ID: 55
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39S ribosomal protein L46, mitochondrialCB [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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GTEx:  ENSG00000259494 
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Entity ID: 56
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39S ribosomal protein L49, mitochondrialDB [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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GTEx:  ENSG00000149792 
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Entity ID: 57
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39S ribosomal protein L51, mitochondrialEB [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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GTEx:  ENSG00000111639 
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Entity ID: 58
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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
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39S ribosomal protein L55, mitochondrialGB [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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GTEx:  ENSG00000162910 
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Entity ID: 60
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Ribosomal protein 63, mitochondrialHB [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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GTEx:  ENSG00000173141 
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Entity ID: 61
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Growth arrest and DNA damage-inducible proteins-interacting protein 1IB [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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GTEx:  ENSG00000179271 
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Entity ID: 62
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39S ribosomal protein S18a, mitochondrialJB [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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GTEx:  ENSG00000096080 
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Entity ID: 63
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39S ribosomal protein L11, mitochondrialKB [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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GTEx:  ENSG00000174547 
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Entity ID: 64
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39S ribosomal protein L10, mitochondrialLB [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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GTEx:  ENSG00000159111 
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Entity ID: 65
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39S ribosomal protein L16, mitochondrialMB [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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GTEx:  ENSG00000166902 
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Entity ID: 66
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Mitochondrial ribosomal protein L18, isoform CRA_bNB [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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Entity ID: 67
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39S ribosomal protein L23, mitochondrialOB [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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GTEx:  ENSG00000214026 
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Entity ID: 68
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39S ribosomal protein L24, mitochondrialPB [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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GTEx:  ENSG00000143314 
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Entity ID: 69
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39S ribosomal protein L3, mitochondrialQB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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GTEx:  ENSG00000114686 
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Entity ID: 70
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39S ribosomal protein L37, mitochondrialRB [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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GTEx:  ENSG00000116221 
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Entity ID: 71
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39S ribosomal protein L38, mitochondrialSB [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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GTEx:  ENSG00000204316 
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Entity ID: 72
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39S ribosomal protein L39, mitochondrialTB [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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GTEx:  ENSG00000154719 
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Entity ID: 73
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39S ribosomal protein L41, mitochondrialUB [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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GTEx:  ENSG00000182154 
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Entity ID: 74
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39S ribosomal protein L42, mitochondrialVB [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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GTEx:  ENSG00000198015 
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Entity ID: 75
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39S ribosomal protein L44, mitochondrialWB [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 76
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39S ribosomal protein L45, mitochondrialXB [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 77
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39S ribosomal protein L48, mitochondrialYB [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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GTEx:  ENSG00000175581 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialZB [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Find proteins for Q8N5N7 (Homo sapiens)
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Go to UniProtKB:  Q8N5N7
PHAROS:  Q8N5N7
GTEx:  ENSG00000136897 
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UniProt GroupQ8N5N7
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialAC [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EL3 (Homo sapiens)
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Go to UniProtKB:  Q96EL3
GTEx:  ENSG00000204822 
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UniProt GroupQ96EL3
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialBC [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P161 (Homo sapiens)
Explore Q6P161 
Go to UniProtKB:  Q6P161
PHAROS:  Q6P161
GTEx:  ENSG00000183617 
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UniProt GroupQ6P161
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