6ZSD

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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:  
    6ZSB, 6ZSD, 6ZSC, 6ZSE

  • 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 ...

    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, mitochondrial0188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrial165Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
Find proteins for O75394 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrial292Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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PHAROS  Q9BQ48
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrial3188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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PHAROS  Q9NZE8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrial4103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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PHAROS  Q9P0J6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrial5423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrial6380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrial7338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrial8206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrial9137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialA1323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1A2118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialA4634Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialAB296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialAC167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 20
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28S ribosomal protein S5, mitochondrialAD430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialAE125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialAF242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialAG396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialAH201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialAI194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S12, mitochondrialAJ138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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PHAROS  O15235
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialAK128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialAL257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialAM137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialAN130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialAO258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialAP142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
MRPS21 isoform 1AQ86Pongo abeliiMutation(s): 0 
Gene Names: CR201_G0018851
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Entity ID: 35
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28S ribosomal protein S23, mitochondrialAS190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialAT173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialAU205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialAV414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialAW187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 40
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28S ribosomal protein S29, mitochondrialAX348Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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Entity ID: 41
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28S ribosomal protein S31, mitochondrialAY395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 42
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28S ribosomal protein S33, mitochondrialAZ106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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Entity ID: 44
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39S ribosomal protein L2, mitochondrialXD305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 45
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39S ribosomal protein L3, mitochondrialXE348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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PHAROS  P09001
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Entity ID: 47
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39S ribosomal protein L9, mitochondrialXH267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 48
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39S ribosomal protein L10, mitochondrialXI261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 49
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39S ribosomal protein L11, mitochondrialXJ192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
Find proteins for Q9Y3B7 (Homo sapiens)
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Entity ID: 52
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39S ribosomal protein L15, mitochondrialXM296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
Find proteins for Q9P015 (Homo sapiens)
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PHAROS  Q9P015
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Entity ID: 53
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39S ribosomal protein L16, mitochondrialXN251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 55
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Mitochondrial ribosomal protein L18, isoform CRA_bXP179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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Entity ID: 56
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39S ribosomal protein L19, mitochondrialXQ292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
Find proteins for P49406 (Homo sapiens)
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PHAROS  P49406
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Entity ID: 57
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39S ribosomal protein L20, mitochondrialXR149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
Find proteins for Q9BYC9 (Homo sapiens)
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PHAROS  Q9BYC9
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Entity ID: 58
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39S ribosomal protein L21, mitochondrialXS205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 59
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39S ribosomal protein L22, mitochondrialXT212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 61
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39S ribosomal protein L24, mitochondrialXV216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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PHAROS  Q96A35
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Entity ID: 62
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39S ribosomal protein L27, mitochondrialXW148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
Find proteins for Q9P0M9 (Homo sapiens)
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PHAROS  Q9P0M9
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Entity ID: 63
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39S ribosomal protein L28, mitochondrialXX256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
Find proteins for Q13084 (Homo sapiens)
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PHAROS  Q13084
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Entity ID: 64
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39S ribosomal protein L47, mitochondrialXY250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
Find proteins for Q9HD33 (Homo sapiens)
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PHAROS  Q9HD33
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Entity ID: 65
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39S ribosomal protein L30, mitochondrialXZ161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
Find proteins for Q8TCC3 (Homo sapiens)
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PHAROS  Q8TCC3
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Entity ID: 66
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39S ribosomal protein L42, mitochondriala142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
Find proteins for Q9Y6G3 (Homo sapiens)
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PHAROS  Q9Y6G3
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Entity ID: 67
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39S ribosomal protein L43, mitochondrialb215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
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PHAROS  Q8N983
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Entity ID: 68
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39S ribosomal protein L44, mitochondrialc332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
Find proteins for Q9H9J2 (Homo sapiens)
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PHAROS  Q9H9J2
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Entity ID: 69
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39S ribosomal protein L45, mitochondriald252Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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PHAROS  Q9BRJ2
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Entity ID: 70
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39S ribosomal protein L46, mitochondriale279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 71
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39S ribosomal protein L48, mitochondrialf212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
Find proteins for Q96GC5 (Homo sapiens)
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PHAROS  Q96GC5
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Entity ID: 72
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39S ribosomal protein L49, mitochondrialg166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
Find proteins for Q13405 (Homo sapiens)
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PHAROS  Q13405
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Entity ID: 73
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39S ribosomal protein L50, mitochondrialh158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens)
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PHAROS  Q8N5N7
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Entity ID: 74
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39S ribosomal protein L51, mitochondriali128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
Find proteins for Q4U2R6 (Homo sapiens)
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PHAROS  Q4U2R6
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Entity ID: 76
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39S ribosomal protein L53, mitochondrialk112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
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PHAROS  Q96EL3
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Entity ID: 77
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39S ribosomal protein L54, mitochondriall138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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PHAROS  Q6P161
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Entity ID: 78
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39S ribosomal protein L55, mitochondrialm128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
Find proteins for Q7Z7F7 (Homo sapiens)
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PHAROS  Q7Z7F7
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Entity ID: 79
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Ribosomal protein 63, mitochondrialo102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
Find proteins for Q9BQC6 (Homo sapiens)
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PHAROS  Q9BQC6
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Entity ID: 80
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Peptidyl-tRNA hydrolase ICT1, mitochondrialp206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
Find proteins for Q14197 (Homo sapiens)
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PHAROS  Q14197
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Entity ID: 81
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Growth arrest and DNA damage-inducible proteins-interacting protein 1q198Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
Find proteins for Q8TAE8 (Homo sapiens)
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PHAROS  Q8TAE8
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Entity ID: 83
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39S ribosomal protein S30, mitochondrials439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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PHAROS  Q9NP92
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Entity ID: 12
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28S ribosomal protein S34, mitochondrialA0218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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PHAROS  P82930
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Entity ID: 15
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Aurora kinase A-interacting proteinA3199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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PHAROS  Q9NWT8
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Entity ID: 34
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28S ribosomal protein S22, mitochondrialAR360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
Find proteins for P82650 (Homo sapiens)
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PHAROS  P82650
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Entity ID: 46
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39S ribosomal protein L4, mitochondrialXF311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
Find proteins for Q9BYD3 (Homo sapiens)
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PHAROS  Q9BYD3
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Entity ID: 50
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39S ribosomal protein L13, mitochondrialXK178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
Find proteins for Q9BYD1 (Homo sapiens)
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PHAROS  Q9BYD1
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Entity ID: 51
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39S ribosomal protein L14, mitochondrialXL145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
Find proteins for Q6P1L8 (Homo sapiens)
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PHAROS  Q6P1L8
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Entity ID: 54
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39S ribosomal protein L17, mitochondrialXO175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
Find proteins for Q9NRX2 (Homo sapiens)
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PHAROS  Q9NRX2
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Entity ID: 60
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39S ribosomal protein L23, mitochondrialXU153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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PHAROS  Q16540
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAj123Homo sapiensMutation(s): 0 
Find proteins for A8K7J6 (Homo sapiens)
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Entity ID: 82
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39S ribosomal protein S18a, mitochondrialr196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens)
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PHAROS  Q9NVS2
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Entity ID: 84
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39S ribosomal protein L12, mitochondrialt1t2t3t4t5t6198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
Find proteins for P52815 (Homo sapiens)
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PHAROS  P52815
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Entity ID: 11
MoleculeChainsLengthOrganismImage
16S rRNAXA1559Homo sapiens
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Entity ID: 17
MoleculeChainsLengthOrganismImage
12SrRNAAA951Homo sapiens
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Entity ID: 43
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mt-tRNAValXB73Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H8Q
Query on H8Q

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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
Query on DOL

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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
Query on GTP

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AX
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
P5P
Query on P5P

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1, 8, A2, AA, AF, AG, XA, q
PURINE RIBOSIDE-5'-MONOPHOSPHATE
C10 H13 N4 O7 P
MCWDCZIDTUQRHK-FDDDBJFASA-N
 Ligand Interaction
Y5P
Query on Y5P

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1, 8, AA, AD, AF, AG, XA, XN, q
1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine
C9 H15 N2 O7 P
ZGXCQKJYIKURPN-FNCVBFRFSA-N
 Ligand Interaction
ZN
Query on ZN

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0, 4, AB, AO, AP, AT, XI
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, XA, XD, XE, XI, XM, XW, g
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research Council--
European Research Council (ERC)--
Knut and Alice Wallenberg Foundation--
European Molecular Biology Organization (EMBO)--

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release