6ZM6

Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

Mechanism of membrane-tethered mitochondrial protein synthesis

Itoh, Y.Andrell, J.Choi, A.Richter, U.Maiti, P.Barrientos, A.Battersby, B.J.Amunts, A.

(2021) Science 


Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialD305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialE348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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PHAROS  P09001
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialF311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialH267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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PHAROS  Q9BYD2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialI261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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PHAROS  Q7Z7H8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialJ192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialK177Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialL145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialM296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialN251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialO175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialP180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialQ292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialR149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L21, mitochondrialS205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialT206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L23, mitochondrialU152Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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PHAROS  Q16540
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialV216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
Find proteins for Q96A35 (Homo sapiens)
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PHAROS  Q96A35
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialW148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
Find proteins for Q9P0M9 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L28, mitochondrialX256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
Find proteins for Q13084 (Homo sapiens)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialY250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
Find proteins for Q9HD33 (Homo sapiens)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialZ161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrial0188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
Find proteins for Q9BYC8 (Homo sapiens)
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PHAROS  Q9BYC8
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Entity ID: 26
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: 27
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L34, mitochondrial292Homo sapiensMutation(s): 0 
Gene Names: MRPL34
Find proteins for Q9BQ48 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L35, mitochondrial3188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
Find proteins for Q9NZE8 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrial4103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
Find proteins for Q9P0J6 (Homo sapiens)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrial5423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrial6380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrial7338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
Find proteins for Q9NYK5 (Homo sapiens)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrial8206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrial9137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondriala142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
Find proteins for Q9Y6G3 (Homo sapiens)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialb214Homo sapiensMutation(s): 0 
Gene Names: MRPL43
Find proteins for Q8N983 (Homo sapiens)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
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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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondriald306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondriale279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialf212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialg166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
Find proteins for Q13405 (Homo sapiens)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialh158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
Find proteins for Q8N5N7 (Homo sapiens)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondriali128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L52, mitochondrialj123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
Find proteins for Q86TS9 (Homo sapiens)
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialk111Homo sapiensMutation(s): 0 
Gene Names: MRPL53
Find proteins for Q96EL3 (Homo sapiens)
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondriall138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialm128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialo102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
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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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1q222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialr196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrials439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrialt1t2t3t4t5t6198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S2, mitochondrialAB296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
Find proteins for Q9Y399 (Homo sapiens)
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S24, mitochondrialAC167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialAD430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
Find proteins for P82675 (Homo sapiens)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S6, mitochondrialAE125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
Find proteins for P82932 (Homo sapiens)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialAF242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialAG396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialAH201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialAI194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
Find proteins for P82912 (Homo sapiens)
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Entity ID: 63
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: 64
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialAK128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
Find proteins for O60783 (Homo sapiens)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialAL257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S16, mitochondrialAM137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialAN130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18b, mitochondrialAO258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
Find proteins for Q9Y676 (Homo sapiens)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S18c, mitochondrialAP142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialAQ86Homo sapiensMutation(s): 0 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S22, mitochondrialAR360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
Find proteins for P82650 (Homo sapiens)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialAS190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialAT173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialAU205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialAV414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
Find proteins for Q92552 (Homo sapiens)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialAW187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialAX398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialAY395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
Find proteins for Q92665 (Homo sapiens)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialAZ106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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Entity ID: 80
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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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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialA1323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
Coiled-coil-helix-coiled-coil-helix domain-containing protein 1A2117Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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PHAROS  Q96BP2
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Aurora kinase A-interacting proteinA3199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialA4689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
Find proteins for Q96EY7 (Homo sapiens)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S mitochondrial rRNAA1561Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mitochondrial tRNAValB72Homo sapiens
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Entity ID: 54
MoleculeChainsLengthOrganismImage
12S mitochondrial rRNAAA954Homo sapiens
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Entity ID: 85
MoleculeChainsLengthOrganismImage
A-site tRNAw68Homo sapiens
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Entity ID: 86
MoleculeChainsLengthOrganismImage
P-site tRNAx70Homo sapiens
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  • Entity ID: 87
    MoleculeChainsLengthOrganismImage
    mRNAy19Homo sapiens
    Small Molecules
    Ligands 6 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GTP
    Query on GTP

    Download Ideal Coordinates CCD File 
    AX
    GUANOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O14 P3
    XKMLYUALXHKNFT-UUOKFMHZSA-N
     Ligand Interaction
    ATP
    Query on ATP

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    AX
    ADENOSINE-5'-TRIPHOSPHATE
    C10 H16 N5 O13 P3
    ZKHQWZAMYRWXGA-KQYNXXCUSA-N
     Ligand Interaction
    FES
    Query on FES

    Download Ideal Coordinates CCD File 
    AP, AT, r
    FE2/S2 (INORGANIC) CLUSTER
    Fe2 S2
    NIXDOXVAJZFRNF-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    0, 4, AO
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

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    A, AA, M, P, i, o
    POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    A, A3, AA, AB, AX, D, E, g, o
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  3 Unique
    IDChainsTypeFormula2D DiagramParent
    SAC
    Query on SAC
    KL-PEPTIDE LINKINGC5 H9 N O4SER
    AYA
    Query on AYA
    UL-PEPTIDE LINKINGC5 H9 N O3ALA
    THC
    Query on THC
    bL-PEPTIDE LINKINGC6 H11 N O4THR
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.59 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    European Research Council (ERC)Sweden--

    Revision History 

    • Version 1.0: 2021-01-13
      Type: Initial release