3J9M

Structure of the human mitochondrial ribosome (class 1)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Ribosome. The structure of the human mitochondrial ribosome.

Amunts, A., Brown, A., Toots, J., Scheres, S.H., Ramakrishnan, V.

(2015) Science 348: 95-98

  • DOI: https://doi.org/10.1126/science.aaa1193
  • Primary Citation of Related Structures:  
    3J9M

  • PubMed Abstract: 

    • The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy ...

    The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. We have determined the structure of the intact mitoribosome to 3.5 angstrom resolution by means of single-particle electron cryogenic microscopy. It reveals 80 extensively interconnected proteins, 36 of which are specific to mitochondria, and three ribosomal RNA molecules. The head domain of the small subunit, particularly the messenger (mRNA) channel, is highly remodeled. Many intersubunit bridges are specific to the mitoribosome, which adopts conformations involving ratcheting or rolling of the small subunit that are distinct from those seen in bacteria or eukaryotes. An intrinsic guanosine triphosphatase mediates a contact between the head and central protuberance. The structure provides a reference for analysis of mutations that cause severe pathologies and for future drug design.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
uL2mC [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2, CGI-22
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Entity ID: 4
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uL3mD [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3, MRL3, RPML3
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Entity ID: 5
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uL4mE [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4, CDABP0091, CGI-28
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Entity ID: 6
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bL9mF [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 7
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uL10mG [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10, MRPL8, RPML8
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Entity ID: 8
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uL11mH [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11, CGI-113
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Entity ID: 9
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uL13mI [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 10
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uL14mJ [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14, MRPL32, RPML32
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Entity ID: 11
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uL15mK [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15, HSPC145
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Entity ID: 12
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uL16mL [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16, PNAS-111
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Entity ID: 13
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bL17mM [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17, LIP2
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Entity ID: 14
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uL18mN [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18, hCG_34030
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Entity ID: 15
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bL19mO [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19, KIAA0104, MRPL15
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Entity ID: 16
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bL20mP [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
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bL21mQ [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 18
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uL22mR [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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Entity ID: 19
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uL23mS [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23, L23MRP, RPL23L
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uL24mT [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 21
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bL27mU [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27, HSPC250
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Entity ID: 22
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bL28mV [auth X]256Homo sapiensMutation(s): 0 
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Entity ID: 23
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uL29mW [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47, NCM1, CGI-204
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Entity ID: 24
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uL30mX [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30, MRPL28, RPML28, HSPC249
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Entity ID: 25
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bL32mY [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32, HSPC283
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bL33mZ [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33, C2orf1
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bL34mAA [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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bL35mBA [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35, BM-007
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bL36mCA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36, BRIP1
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Entity ID: 30
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mL37DA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37, MRPL2, RPML2, HSPC235
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mL38EA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38, HSPC262
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Entity ID: 32
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mL39FA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39, C21orf92, MRPL5, RPML5, MSTP003, PRED22
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Entity ID: 33
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mL40GA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40, NLVCF, URIM
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mL41HA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41, BMRP, MRPL27, RPML27, PIG3
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mL42IA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42, MRPL31, MRPS32, RPML31, HSPC204, PTD007
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mL43JA [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 37
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mL44KA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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mL45LA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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mL46MA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46, C15orf4, LIECG2
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mL48NA [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48, CGI-118, HSPC290
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Entity ID: 41
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mL49OA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49, C11orf4, NOF1, OK/SW-cl.67
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mL50PA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
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mL51QA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51, MRP64, CDA09, HSPC241
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Entity ID: 44
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mL52RA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 45
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mL53SA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
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mL54TA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
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bL31mUA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55, UNQ5835/PRO19675
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Entity ID: 48
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mL63VA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57, MRP63
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Entity ID: 49
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mL62 (ICT1)WA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58, DS1, ICT1
EC: 3.1.1.29
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Entity ID: 50
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mL64 (CRIF1)XA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1, MRPL59, PLINP1, PRG6
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Entity ID: 51
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mL66 (bS18a)YA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
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mL65 (mS30)ZA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30, PDCD9, BM-047
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Entity ID: 53
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Unknown protein/protein extensionAB [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 56
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uS2mDB [auth AB]296Homo sapiensMutation(s): 0 
Gene Names: MRPS2, CGI-91
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Entity ID: 57
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uS3mEB [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24, HSPC335
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Entity ID: 58
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uS5mFB [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 59
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bS6mGB [auth AE]125Homo sapiensMutation(s): 0 
Gene Names: MRPS6, C21orf101, RPMS6
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Entity ID: 60
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uS7mHB [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 61
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uS9mIB [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9, RPMS9
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Entity ID: 62
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uS10mJB [auth AH]201Homo sapiensMutation(s): 0 
Gene Names: MRPS10, MSTP040
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Entity ID: 63
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uS11mKB [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11, RPMS11, HCC2
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Entity ID: 64
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uS12mLB [auth AJ]138Homo sapiensMutation(s): 0 
Gene Names: MRPS12, RPMS12, RPSM12
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Entity ID: 65
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uS14mMB [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 66
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uS15mNB [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15, RPMS15, DC37
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Entity ID: 67
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bS16mOB [auth AM]137Homo sapiensMutation(s): 0 
Gene Names: MRPS16, RPMS16, CGI-132
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Entity ID: 68
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uS17mPB [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17, RPMS17, HSPC011
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Entity ID: 69
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mS40 (bS18b)QB [auth AO]258Homo sapiensMutation(s): 0 
Gene Names: MRPS18B, C6orf14, HSPC183, PTD017
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Entity ID: 70
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bS18m (bS18c)RB [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18C, CGI-134
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Entity ID: 71
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bS21mSB [auth AQ]87Homo sapiensMutation(s): 0 
Gene Names: MRPS21, RPMS21, MDS016
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Entity ID: 72
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mS22TB [auth AR]360Homo sapiensMutation(s): 0 
Gene Names: MRPS22, C3orf5, RPMS22, GK002
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Entity ID: 73
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mS23UB [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23, CGI-138, HSPC329
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Entity ID: 74
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mS25VB [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25, RPMS25
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Entity ID: 75
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mS26WB [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26, C20orf193, RPMS13
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Entity ID: 76
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mS27XB [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27, KIAA0264
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Entity ID: 77
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bS1mYB [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28, MRPS35, HSPC007
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Entity ID: 78
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mS29ZB [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3, MRPS29
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Entity ID: 79
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mS31AC [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31, IMOGN38
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Entity ID: 80
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mS33BC [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33, CGI-139, PTD003
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Entity ID: 81
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mS34CC [auth A0]218Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 82
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mS35DC [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35, MRPS28, HDCMD11P, MDS023, PSEC0213
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Entity ID: 83
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mS37EC [auth A2]118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1, C10orf34, MRPS37
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