7L08

Cryo-EM structure of the human 55S mitoribosome-RRFmt complex.

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

  • Deposited: 2020-12-11 Released: 2021-05-12 
  • Deposition Author(s): Koripella, R., Agrawal, E.K., Deep, A., 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: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the human mitochondrial ribosome-EF-G2 complex with mtRRF(ClassI)

Koripella, R.K.Agrawal, E.K.Deep, A.Agrawal, R.K.

To be published.

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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Entity ID: 3
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28S ribosomal protein S24, mitochondrialC [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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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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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S11, mitochondrialE [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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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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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S14, mitochondrialG [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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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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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S17, mitochondrialI [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 10
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28S ribosomal protein S18b, mitochondrialJ [auth AO]258Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 11
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28S ribosomal protein S18c, mitochondrialK [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S21, mitochondrialL [auth AQ]87Homo sapiensMutation(s): 1 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S25, mitochondrialM [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S28, mitochondrialN [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S29, mitochondrialO [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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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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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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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S15, mitochondrialR [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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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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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S23, mitochondrialT [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S26, mitochondrialU [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialV [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S31, mitochondrialW [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S33, mitochondrialX [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S35, mitochondrialY [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
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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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Pentatricopeptide repeat domain-containing protein 3, mitochondrialBA [auth A4]689Homo sapiensMutation(s): 0 
Gene Names: PTCD3MRPS39TRG15
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S5, mitochondrialCA [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S7, mitochondrialDA [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S9, mitochondrialEA [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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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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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialIA [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialJA [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialKA [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialLA [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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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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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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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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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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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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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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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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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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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L30, mitochondrialUA [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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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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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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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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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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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L36, mitochondrialZA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L40, mitochondrialAB [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L43, mitochondrialBB [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L46, mitochondrialCB [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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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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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L51, mitochondrialEB [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAFB [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L55, mitochondrialGB [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein 63, mitochondrialHB [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1IB [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S18a, mitochondrialJB [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialKB [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialLB [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialMB [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
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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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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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialQB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrialRB [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L38, mitochondrialSB [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrialTB [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L41, mitochondrialUB [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondrialVB [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialWB [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L45, mitochondrialXB [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialYB [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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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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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L53, mitochondrialAC [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L54, mitochondrialBC [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialCC [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein S30, mitochondrialDC [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialEC [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
P-site fingerFC [auth u]65Homo sapiensMutation(s): 0 
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L12, mitochondrialGC [auth TA], HC [auth TB]198Homo sapiensMutation(s): 0 
Gene Names: MRPL12MRPL7RPML12
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factor, mitochondrialIC [auth z]204Homo sapiensMutation(s): 0 
Gene Names: MRRF
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Entity ID: 1
MoleculeChainsLengthOrganismImage
12S rRNAA [auth AA]954Homo sapiens
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S RRNAFA [auth A]1559Homo sapiens
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Entity ID: 33
MoleculeChainsLengthOrganismImage
tRNAVALGA [auth B]73Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
OD [auth AX]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JH [auth 0], KD [auth AB], KH [auth 4], LD [auth AO], MD [auth AP], MH [auth r], ND [auth AT]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth AA] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , BD [auth AA] , BE [auth A] , BF [auth A] , 
AD [auth AA],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth A],  BD [auth AA],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  CD [auth AA],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  DD [auth AA],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth A],  ED [auth AA],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  FD [auth AA],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  GD [auth AA],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth D],  HD [auth AA],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth M],  ID [auth AA],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth W],  JC [auth AA],  JD [auth AA],  JE [auth A],  JF [auth A],  JG [auth A],  KC [auth AA],  KE [auth A],  KF [auth A],  KG [auth A],  LC [auth AA],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth g],  MC [auth AA],  ME [auth A],  MF [auth A],  MG [auth A],  NC [auth AA],  NE [auth A],  NF [auth A],  NG [auth A],  NH [auth E],  OC [auth AA],  OE [auth A],  OF [auth A],  OG [auth A],  PC [auth AA],  PD [auth AG],  PE [auth A],  PF [auth A],  PG [auth A],  QC [auth AA],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth A],  RC [auth AA],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth A],  SC [auth AA],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth A],  TC [auth AA],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth A],  UC [auth AA],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth A],  VC [auth AA],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth A],  WC [auth AA],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  XC [auth AA],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  YC [auth AA],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  ZC [auth AA],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesR01 GM61576

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release