6ZSG

Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA and E-site tRNA

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

  • Deposited: 2020-07-15 Released: 2020-10-14 
  • Deposition Author(s): Aibara, S., Singh, V., Modelska, A., Amunts, A.
  • Funding Organization(s): Swedish Research Council, European Research Council (ERC), Knut and Alice Wallenberg Foundation, European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis of mitochondrial translation.

Aibara, S.Singh, V.Modelska, A.Amunts, A.

(2020) Elife 9

  • DOI: 10.7554/eLife.58362
  • Primary Citation of Related Structures:  
    6ZS9, 6ZSA, 6ZSB, 6ZSC, 6ZSD, 6ZSE, 6ZSG, 7OG4

  • PubMed Abstract: 
  • Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear ...

    Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 Å resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrialA [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialB [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrialC [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrialD [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialE [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialF [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialG [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialH [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialI [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialJ [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S34, mitochondrialL [auth A0]218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialM [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1N [auth A2]118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinO [auth A3]199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialP [auth A4]689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialR [auth AB]296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialS [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialT [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialU [auth AE]125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialV [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialW [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialX [auth AH]201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialY [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialZ [auth AJ]138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialAA [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialBA [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialCA [auth AM]137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialDA [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialEA [auth AO]258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialFA [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialGA [auth AQ]86Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialHA [auth AR]360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialIA [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialJA [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialKA [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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Entity ID: 38
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28S ribosomal protein S27, mitochondrialLA [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialMA [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 40
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28S ribosomal protein S29, mitochondrialNA [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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Entity ID: 41
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28S ribosomal protein S31, mitochondrialOA [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialPA [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialRA [auth XD]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialSA [auth XE]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialTA [auth XF]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialUA [auth XH]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialVA [auth XI]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialWA [auth XJ]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialXA [auth XK]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialYA [auth XL]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialZA [auth XM]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 53
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39S ribosomal protein L16, mitochondrialAB [auth XN]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialBB [auth XO]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 55
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39S ribosomal protein L18, mitochondrialCB [auth XP]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 56
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39S ribosomal protein L19, mitochondrialDB [auth XQ]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 57
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39S ribosomal protein L20, mitochondrialEB [auth XR]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 58
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39S ribosomal protein L21, mitochondrialFB [auth XS]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 59
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39S ribosomal protein L22, mitochondrialGB [auth XT]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
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Entity ID: 60
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39S ribosomal protein L23, mitochondrialHB [auth XU]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 61
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39S ribosomal protein L24, mitochondrialIB [auth XV]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 62
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39S ribosomal protein L27, mitochondrialJB [auth XW]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 63
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39S ribosomal protein L28, mitochondrialKB [auth XX]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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Entity ID: 64
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39S ribosomal protein L47, mitochondrialLB [auth XY]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 65
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39S ribosomal protein L30, mitochondrialMB [auth XZ]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 66
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39S ribosomal protein L42, mitochondrialNB [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 67
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39S ribosomal protein L43, mitochondrialOB [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 68
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39S ribosomal protein L44, mitochondrialPB [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 69
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39S ribosomal protein L45, mitochondrialQB [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 70
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39S ribosomal protein L46, mitochondrialRB [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 71
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39S ribosomal protein L48, mitochondrialSB [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 72
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39S ribosomal protein L49, mitochondrialTB [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 73
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39S ribosomal protein L50, mitochondrialUB [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 74
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39S ribosomal protein L51, mitochondrialVB [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 75
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39S ribosomal protein L52, mitochondrialWB [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 76
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39S ribosomal protein L53, mitochondrialXB [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 77
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39S ribosomal protein L54, mitochondrialYB [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 78
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39S ribosomal protein L55, mitochondrialZB [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 79
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Ribosomal protein 63, mitochondrialAC [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 80
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Peptidyl-tRNA hydrolase ICT1, mitochondrialBC [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Entity ID: 81
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Growth arrest and DNA damage-inducible proteins-interacting protein 1CC [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 82
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39S ribosomal protein S18a, mitochondrialDC [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 87
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39S ribosomal protein S30, mitochondrialIC [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Entity ID: 88
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39S ribosomal protein L12, mitochondrialJC [auth t1], KC [auth t2], LC [auth t3], MC [auth t4], NC [auth t5], OC [auth t6]198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
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Entity ID: 11
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16S mitochondrial rRNAK [auth XA]1561Homo sapiens
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Entity ID: 17
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12S mitochondrial rRNAQ [auth AA]954Homo sapiens
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Entity ID: 43
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mitochondrial tRNAValQA [auth XB]72Homo sapiens
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  • Entity ID: 83
    MoleculeChainsLengthOrganismImage
    mRNAEC [auth r1]14Homo sapiens
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    Entity ID: 84
    MoleculeChainsLengthOrganismImage
    A-site tRNAFC [auth r2]76Homo sapiens
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    Entity ID: 85
    MoleculeChainsLengthOrganismImage
    P-site tRNAGC [auth r3]75Homo sapiens
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    Entity ID: 86
    MoleculeChainsLengthOrganismImage
    E-site tRNAHC [auth r4]75Homo sapiens
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    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    H8Q (Subject of Investigation/LOI)
    Query on H8Q

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    EI [auth XA]~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide
    C53 H67 N9 O10 S
    WTHRRGMBUAHGNI-QGNGWGIWSA-N
     Ligand Interaction
    DOL (Subject of Investigation/LOI)
    Query on DOL

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    FI [auth XA]5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE
    C34 H50 N4 O9 S
    SUYRLXYYZQTJHF-VMBLUXKRSA-N
     Ligand Interaction
    GTP (Subject of Investigation/LOI)
    Query on GTP

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    EK [auth AX]GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    AK [auth AB], BK [auth AO], CK [auth AP], DK [auth AT], LK [auth r], PC [auth 0], RC [auth 4]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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