7A5J

Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Elongational stalling activates mitoribosome-associated quality control.

Desai, N.Yang, H.Chandrasekaran, V.Kazi, R.Minczuk, M.Ramakrishnan, V.

(2020) Science 370: 1105-1110

  • DOI: 10.1126/science.abc7782
  • Primary Citation of Related Structures:  
    7A5F, 7A5G, 7A5H, 7A5I, 7A5J, 7A5K

  • PubMed Abstract: 
  • The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3 ...

    The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialA [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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GTEx:  ENSG00000112651 
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Entity ID: 2
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39S ribosomal protein L3, mitochondrialB [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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GTEx:  ENSG00000114686 
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Entity ID: 3
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39S ribosomal protein L4, mitochondrialC [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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GTEx:  ENSG00000105364 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialGB [auth C],
D [auth H]
267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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GTEx:  ENSG00000143436 
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Entity ID: 5
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39S ribosomal protein L10, mitochondrialE [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 6
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39S ribosomal protein L11, mitochondrialF [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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GTEx:  ENSG00000174547 
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Entity ID: 7
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39S ribosomal protein L13, mitochondrialG [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 8
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39S ribosomal protein L14, mitochondrialH [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 9
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39S ribosomal protein L15, mitochondrialI [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 10
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39S ribosomal protein L16, mitochondrialJ [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 11
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39S ribosomal protein L17, mitochondrialK [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 12
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Mitochondrial ribosomal protein L18, isoform CRA_bL [auth P]179Homo sapiensMutation(s): 0 
Gene Names: MRPL18hCG_34030
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Entity ID: 13
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39S ribosomal protein L19, mitochondrialM [auth Q]292Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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GTEx:  ENSG00000115364 
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39S ribosomal protein L20, mitochondrialN [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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GTEx:  ENSG00000242485 
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Entity ID: 15
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39S ribosomal protein L21, mitochondrialO [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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GTEx:  ENSG00000197345 
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Entity ID: 16
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39S ribosomal protein L22, mitochondrialP [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MRPL22
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GTEx:  ENSG00000082515 
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Entity ID: 17
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39S ribosomal protein L23, mitochondrialQ [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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GTEx:  ENSG00000214026 
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Entity ID: 18
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39S ribosomal protein L24, mitochondrialR [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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GTEx:  ENSG00000143314 
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Entity ID: 19
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39S ribosomal protein L27, mitochondrialS [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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GTEx:  ENSG00000108826 
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Entity ID: 20
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39S ribosomal protein L28, mitochondrialT [auth X]256Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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GTEx:  ENSG00000086504 
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Entity ID: 21
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39S ribosomal protein L47, mitochondrialU [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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GTEx:  ENSG00000136522 
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Entity ID: 22
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39S ribosomal protein L30, mitochondrialV [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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GTEx:  ENSG00000185414 
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Entity ID: 23
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39S ribosomal protein L32, mitochondrialW [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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GTEx:  ENSG00000106591 
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Entity ID: 24
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39S ribosomal protein L33, mitochondrialX [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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GTEx:  ENSG00000243147 
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Entity ID: 25
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39S ribosomal protein L34, mitochondrialY [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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GTEx:  ENSG00000130312 
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Entity ID: 26
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39S ribosomal protein L35, mitochondrialZ [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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GTEx:  ENSG00000132313 
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Entity ID: 27
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39S ribosomal protein L36, mitochondrialAA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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GTEx:  ENSG00000171421 
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Entity ID: 28
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39S ribosomal protein L37, mitochondrialBA [auth 5]423Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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GTEx:  ENSG00000116221 
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Entity ID: 29
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39S ribosomal protein L38, mitochondrialCA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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GTEx:  ENSG00000204316 
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Entity ID: 30
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39S ribosomal protein L39, mitochondrialDA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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GTEx:  ENSG00000154719 
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Entity ID: 31
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39S ribosomal protein L40, mitochondrialEA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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GTEx:  ENSG00000185608 
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Entity ID: 32
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39S ribosomal protein L41, mitochondrialFA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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GTEx:  ENSG00000182154 
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Entity ID: 33
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39S ribosomal protein L42, mitochondrialGA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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GTEx:  ENSG00000198015 
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Entity ID: 34
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39S ribosomal protein L43, mitochondrialHA [auth b]155Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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GTEx:  ENSG00000055950 
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Entity ID: 35
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39S ribosomal protein L44, mitochondrialIA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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GTEx:  ENSG00000135900 
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Entity ID: 36
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39S ribosomal protein L45, mitochondrialJA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 37
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39S ribosomal protein L46, mitochondrialKA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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GTEx:  ENSG00000259494 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L48, mitochondrialLA [auth f]194Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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GTEx:  ENSG00000175581 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L49, mitochondrialMA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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GTEx:  ENSG00000149792 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialNA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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GTEx:  ENSG00000136897 
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Entity ID: 41
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39S ribosomal protein L51, mitochondrialOA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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GTEx:  ENSG00000111639 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal protein L52 (MRPL52), transcript variant 1, mRNAPA [auth j]123Homo sapiensMutation(s): 0 
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Entity ID: 43
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39S ribosomal protein L53, mitochondrialQA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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GTEx:  ENSG00000204822 
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Entity ID: 44
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39S ribosomal protein L54, mitochondrialRA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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GTEx:  ENSG00000183617 
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Entity ID: 45
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39S ribosomal protein L55, mitochondrialSA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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GTEx:  ENSG00000162910 
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Entity ID: 46
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Ribosomal protein 63, mitochondrialTA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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GTEx:  ENSG00000173141 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-tRNA hydrolase ICT1, mitochondrialUA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Find proteins for Q14197 (Homo sapiens)
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GTEx:  ENSG00000167862 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Growth arrest and DNA damage-inducible proteins-interacting protein 1VA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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GTEx:  ENSG00000179271 
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Entity ID: 49
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39S ribosomal protein S18a, mitochondrialWA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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GTEx:  ENSG00000096080 
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Entity ID: 50
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39S ribosomal protein S30, mitochondrialXA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
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Find proteins for Q9NP92 (Homo sapiens)
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GTEx:  ENSG00000112996 
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Entity ID: 51
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Unknown protein/protein extensionYA [auth t]28Homo sapiensMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Mitochondrial assembly of ribosomal large subunit protein 1ZA [auth u]234Homo sapiensMutation(s): 0 
Gene Names: MALSU1C7orf30
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GTEx:  ENSG00000156928 
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Entity ID: 53
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MIEF1 upstream open reading frame proteinAB [auth v]70Homo sapiensMutation(s): 0 
Gene Names: MIEF1
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Entity ID: 54
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Acyl carrier protein, mitochondrialBB [auth w]156Homo sapiensMutation(s): 0 
Gene Names: NDUFAB1
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GTEx:  ENSG00000004779 
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Entity ID: 55
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50S ribosomal protein L1CB [auth n]229Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
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Find proteins for Q72GV9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
nascent chainFB [auth Y2]29Homo sapiensMutation(s): 0 
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Entity ID: 60
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Unknown protein/protein extensionIB [auth y]32Homo sapiensMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
unknown protein/protein extensionJB [auth z]14Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChainsLengthOrganismImage
16S rRNADB [auth A]1559Homo sapiens
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Entity ID: 57
MoleculeChainsLengthOrganismImage
mt-tRNAValEB [auth B]69Homo sapiens
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Entity ID: 59
MoleculeChainsLengthOrganismImage
mt-tRNAHB [auth G],
KB [auth x]
73Homo sapiens
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNS
Query on PNS

Download Ideal Coordinates CCD File 
QB [auth v]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MB [auth 0],
NB [auth 4],
PB [auth r]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
RB [auth n],
SB [auth n]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BC [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LB [auth D],
LC [auth A],
LD [auth A],
LE [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
OB [auth g],
OC [auth A],
OD [auth A],
OE [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
TB [auth n],
UB [auth n],
VB [auth n],
ZB [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
Louis-Jeantet FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release