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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
uL2mC [auth D]305Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112651 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uL3mD [auth E]348Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114686 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL4mE [auth F]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105364 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
bL9mF [auth H]267Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143436 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL10mG [auth I]261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159111 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL11mH [auth J]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174547 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mI [auth K]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172172 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mJ [auth L]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180992 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mK [auth M]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137547 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL16mL [auth N]251Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166902 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mM [auth O]175Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000158042 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL18mN [auth P]179Homo sapiensMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mO [auth Q]292Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115364 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
bL20mP [auth R]149Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000242485 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mQ [auth S]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197345 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mR [auth T]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000082515 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mS [auth U]153Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000214026 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mT [auth V]216Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143314 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
bL27mU [auth W]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108826 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mV [auth X]256Homo sapiensMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mW [auth Y]250Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136522 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mX [auth Z]161Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185414 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mY [auth 0]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106591 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
bL33mZ [auth 1]65Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243147 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
bL34mAA [auth 2]92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130312 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mBA [auth 3]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132313 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
bL36mCA [auth 4]103Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171421 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mL37DA [auth 5]423Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116221 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL38EA [auth 6]380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204316 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mL39FA [auth 7]338Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000154719 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mL40GA [auth 8]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185608 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL41HA [auth 9]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182154 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mL42IA [auth a]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198015 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mL43JA [auth b]155Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000055950 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mL44KA [auth c]332Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135900 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mL45LA [auth d]306Homo sapiensMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mL46MA [auth e]279Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000259494 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL48NA [auth f]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175581 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mL49OA [auth g]166Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149792 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mL50PA [auth h]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136897 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL51QA [auth i]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111639 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mL52RA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mL53SA [auth k]112Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204822 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL54TA [auth l]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000183617 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
bL31mUA [auth m]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162910 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mL63VA [auth o]102Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173141 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL62 (ICT1)WA [auth p]206Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167862 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL64 (CRIF1)XA [auth q]222Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000179271 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mL66 (bS18a)YA [auth r]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000096080 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mL65 (mS30)ZA [auth s]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112996 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein/protein extensionAB [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
uS2mDB [auth AB]296Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122140 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS3mEB [auth AC]167Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000062582 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
uS5mFB [auth AD]430Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144029 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mGB [auth AE]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000243927 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
uS7mHB [auth AF]242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125445 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mIB [auth AG]396Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000135972 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mJB [auth AH]201Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000048544 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mKB [auth AI]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181991 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS12mLB [auth AJ]138Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128626 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mMB [auth AK]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000120333 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mNB [auth AL]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116898 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mOB [auth AM]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182180 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mPB [auth AN]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000239789 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
mS40 (bS18b)QB [auth AO]258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204568 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
bS18m (bS18c)RB [auth AP]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163319 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mSB [auth AQ]87Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000266472 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
mS22TB [auth AR]360Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175110 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
mS23UB [auth AS]190Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000181610 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mS25VB [auth AT]173Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131368 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
mS26WB [auth AU]205Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125901 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
mS27XB [auth AV]414Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000113048 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
bS1mYB [auth AW]187Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147586 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
mS29ZB [auth AX]398Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132676 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
mS31AC [auth AY]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102738 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
mS33BC [auth AZ]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000090263 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
mS34CC [auth A0]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000074071 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
mS35DC [auth A1]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000061794 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
mS37EC [auth A2]118Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172586 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
mS38FC [auth A3]199Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175756 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
mS39GC [auth A4]579Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000132300 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,559Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
mt-tRNAVal73Homo sapiens
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Entity ID: 54
MoleculeChains LengthOrganismImage
E-site tRNABB [auth u]2Homo sapiens
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Entity ID: 55
MoleculeChains LengthOrganismImage
12S rRNACB [auth AA]954Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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LH [auth AX]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN

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BG [auth 0]
CG [auth 4]
EG [auth r]
HH [auth AB]
IH [auth AO]
BG [auth 0],
CG [auth 4],
EG [auth r],
HH [auth AB],
IH [auth AO],
JH [auth AP],
KH [auth AT]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection