6NU3

Structural insights into unique features of the human mitochondrial ribosome recycling

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-01-30 Released: 2019-04-17 
  • Deposition Author(s): Sharma, M.R., Koripella, R.K., 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: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into unique features of the human mitochondrial ribosome recycling.

Koripella, R.K.Sharma, M.R.Risteff, P.Keshavan, P.Agrawal, R.K.

(2019) Proc Natl Acad Sci U S A 116: 8283-8288

  • DOI: https://doi.org/10.1073/pnas.1815675116
  • Primary Citation of Related Structures:  
    6NU2, 6NU3

  • PubMed Abstract: 
  • Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts ...

    Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRF mt ) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRF mt Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRF mt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRF mt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.


    Organizational Affiliation

    Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialC [auth D]305Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialD [auth E]348Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialE [auth F]311Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialF [auth H]267Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialG [auth I]261Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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Entity ID: 8
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39S ribosomal protein L11, mitochondrialH [auth J]192Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 9
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39S ribosomal protein L13, mitochondrialI [auth K]178Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 10
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39S ribosomal protein L14, mitochondrialJ [auth L]145Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 11
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39S ribosomal protein L15, mitochondrialK [auth M]296Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 12
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39S ribosomal protein L16, mitochondrialL [auth N]251Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 13
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39S ribosomal protein L17, mitochondrialM [auth O]175Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 14
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39S ribosomal protein L18, mitochondrialN [auth P]180Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 15
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39S ribosomal protein L19, mitochondrialO [auth Q]219Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 16
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39S ribosomal protein L20, mitochondrialP [auth R]149Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
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39S ribosomal protein L21, mitochondrialQ [auth S]205Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 18
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39S ribosomal protein L22, mitochondrialR [auth T]206Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
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Entity ID: 19
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39S ribosomal protein L23, mitochondrialS [auth U]153Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
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Entity ID: 20
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39S ribosomal protein L24, mitochondrialT [auth V]216Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 21
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39S ribosomal protein L27, mitochondrialU [auth W]148Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 22
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39S ribosomal protein L28, mitochondrialV [auth X]243Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
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Entity ID: 23
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39S ribosomal protein L47, mitochondrialW [auth Y]250Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 24
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39S ribosomal protein L30, mitochondrialX [auth Z]161Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
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Entity ID: 25
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39S ribosomal protein L32, mitochondrialY [auth 0]188Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 26
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39S ribosomal protein L33, mitochondrialZ [auth 1]65Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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39S ribosomal protein L34, mitochondrialAA [auth 2]92Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 28
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39S ribosomal protein L35, mitochondrialBA [auth 3]188Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 29
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39S ribosomal protein L36, mitochondrialCA [auth 4]103Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 30
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39S ribosomal protein L37, mitochondrialDA [auth 5]394Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 31
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39S ribosomal protein L38, mitochondrialEA [auth 6]380Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 32
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39S ribosomal protein L39, mitochondrialFA [auth 7]338Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 33
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39S ribosomal protein L40, mitochondrialGA [auth 8]206Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
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Entity ID: 34
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39S ribosomal protein L41, mitochondrialHA [auth 9]137Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
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Entity ID: 35
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39S ribosomal protein L42, mitochondrialIA [auth a]142Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 36
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39S ribosomal protein L43, mitochondrialJA [auth b]215Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 37
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39S ribosomal protein L44, mitochondrialKA [auth c]332Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 38
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cDNA FLJ61100, highly similar to 39S ribosomal protein L45, mitochondrialLA [auth d]306Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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39S ribosomal protein L46, mitochondrialMA [auth e]279Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
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39S ribosomal protein L48, mitochondrialNA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 41
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39S ribosomal protein L49, mitochondrialOA [auth g]166Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 42
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39S ribosomal protein L50, mitochondrialPA [auth h]158Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
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39S ribosomal protein L51, mitochondrialQA [auth i]128Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 44
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39S ribosomal protein L52, mitochondrialRA [auth j]123Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 45
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39S ribosomal protein L53, mitochondrialSA [auth k]112Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
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39S ribosomal protein L54, mitochondrialTA [auth l]138Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
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39S ribosomal protein L55, mitochondrialUA [auth m]128Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 48
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Ribosomal protein 63, mitochondrialVA [auth o]102Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
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Entity ID: 49
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Peptidyl-tRNA hydrolase ICT1, mitochondrialWA [auth p]206Homo sapiensMutation(s): 0 
Gene Names: MRPL58DS1ICT1
EC: 3.1.1.29
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Entity ID: 50
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Growth arrest and DNA damage-inducible proteins-interacting protein 1XA [auth q]222Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 51
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39S ribosomal protein S18a, mitochondrialYA [auth r]196Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
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Entity ID: 52
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39S ribosomal protein S30, mitochondrialZA [auth s]439Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-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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28S ribosomal protein S2, mitochondrialDB [auth AB]296Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
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Entity ID: 57
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28S ribosomal protein S24, mitochondrialEB [auth AC]167Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 58
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28S ribosomal protein S5, mitochondrialFB [auth AD]430Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 59
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28S ribosomal protein S6, mitochondrialGB [auth AE]125Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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Entity ID: 60
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28S ribosomal protein S7, mitochondrialHB [auth AF]242Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 61
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28S ribosomal protein S9, mitochondrialIB [auth AG]396Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
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Entity ID: 62
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28S ribosomal protein S10, mitochondrialJB [auth AH]201Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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Entity ID: 63
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28S ribosomal protein S11, mitochondrialKB [auth AI]194Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
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Entity ID: 64
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28S ribosomal protein S12, mitochondrialLB [auth AJ]138Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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Entity ID: 65
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28S ribosomal protein S14, mitochondrialMB [auth AK]128Homo sapiensMutation(s): 0 
Gene Names: MRPS14
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Entity ID: 66
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28S ribosomal protein S15, mitochondrialNB [auth AL]257Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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Entity ID: 67
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28S ribosomal protein S16, mitochondrialOB [auth AM]137Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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Entity ID: 68
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28S ribosomal protein S17, mitochondrialPB [auth AN]130Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 69
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28S ribosomal protein S18b, mitochondrialQB [auth AO]185Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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Entity ID: 70
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28S ribosomal protein S18c, mitochondrialRB [auth AP]142Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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Entity ID: 71
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28S ribosomal protein S21, mitochondrialSB [auth AQ]86Homo sapiensMutation(s): 0 
Gene Names: MRPS21RPMS21MDS016
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Entity ID: 72
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28S ribosomal protein S22, mitochondrialTB [auth AR]360Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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Entity ID: 73
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28S ribosomal protein S23, mitochondrialUB [auth AS]190Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
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Entity ID: 74
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28S ribosomal protein S25, mitochondrialVB [auth AT]173Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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Entity ID: 75
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28S ribosomal protein S26, mitochondrialWB [auth AU]205Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
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Entity ID: 76
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28S ribosomal protein S27, mitochondrialXB [auth AV]414Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
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Entity ID: 77
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28S ribosomal protein S28, mitochondrialYB [auth AW]187Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
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Entity ID: 78
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28S ribosomal protein S29, mitochondrialZB [auth AX]398Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
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Entity ID: 79
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28S ribosomal protein S31, mitochondrialAC [auth AY]395Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
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Entity ID: 80
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28S ribosomal protein S33, mitochondrialBC [auth AZ]106Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
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Entity ID: 81
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28S ribosomal protein S34, mitochondrialCC [auth A0]225Homo sapiensMutation(s): 0 
Gene Names: MRPS34
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Entity ID: 82
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28S ribosomal protein S35, mitochondrialDC [auth A1]323Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
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Entity ID: 83
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Coiled-coil-helix-coiled-coil-helix domain-containing protein 1EC [auth A2]118Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
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Entity ID: 84
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Aurora kinase A-interacting proteinFC [auth A3]199Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
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Find proteins for Q9NWT8 (Homo sapiens)
Explore Q9NWT8 
Go to UniProtKB:  Q9NWT8
PHAROS:  Q9NWT8
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