6NU2

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), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 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 mit ...

    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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L3, mitochondrialE304Homo sapiensMutation(s): 0 
Gene Names: MRPL3MRL3RPML3
Find proteins for P09001 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialF250Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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PHAROS  Q9BYD3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L9, mitochondrialH95Homo sapiensMutation(s): 0 
Gene Names: MRPL9
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PHAROS  Q9BYD2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L10, mitochondrialI168Homo sapiensMutation(s): 0 
Gene Names: MRPL10MRPL8RPML8
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PHAROS  Q7Z7H8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialJ140Homo sapiensMutation(s): 0 
Gene Names: MRPL11CGI-113
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L13, mitochondrialK177Homo sapiensMutation(s): 0 
Gene Names: MRPL13
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L14, mitochondrialL115Homo sapiensMutation(s): 0 
Gene Names: MRPL14MRPL32RPML32
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L15, mitochondrialM287Homo sapiensMutation(s): 0 
Gene Names: MRPL15HSPC145
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialN205Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 13
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39S ribosomal protein L17, mitochondrialO152Homo sapiensMutation(s): 0 
Gene Names: MRPL17LIP2
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L18, mitochondrialP138Homo sapiensMutation(s): 0 
Gene Names: MRPL18HSPC071
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L19, mitochondrialQ219Homo sapiensMutation(s): 0 
Gene Names: MRPL19KIAA0104MRPL15
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L20, mitochondrialR140Homo sapiensMutation(s): 0 
Gene Names: MRPL20
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Entity ID: 17
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39S ribosomal protein L21, mitochondrialS156Homo sapiensMutation(s): 0 
Gene Names: MRPL21
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Entity ID: 20
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39S ribosomal protein L24, mitochondrialV202Homo sapiensMutation(s): 0 
Gene Names: MRPL24
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Entity ID: 21
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39S ribosomal protein L27, mitochondrialW115Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L47, mitochondrialY176Homo sapiensMutation(s): 0 
Gene Names: MRPL47NCM1CGI-204
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L32, mitochondrial0108Homo sapiensMutation(s): 0 
Gene Names: MRPL32HSPC283
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrial152Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 27
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39S ribosomal protein L34, mitochondrial246Homo sapiensMutation(s): 0 
Gene Names: MRPL34
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Entity ID: 28
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39S ribosomal protein L35, mitochondrial395Homo sapiensMutation(s): 0 
Gene Names: MRPL35BM-007
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Entity ID: 29
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39S ribosomal protein L36, mitochondrial436Homo sapiensMutation(s): 0 
Gene Names: MRPL36BRIP1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L37, mitochondrial5392Homo sapiensMutation(s): 0 
Gene Names: MRPL37MRPL2RPML2HSPC235
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Entity ID: 31
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39S ribosomal protein L38, mitochondrial6354Homo sapiensMutation(s): 0 
Gene Names: MRPL38HSPC262
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L39, mitochondrial7287Homo sapiensMutation(s): 0 
Gene Names: MRPL39C21orf92MRPL5RPML5MSTP003PRED22
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L42, mitochondriala108Homo sapiensMutation(s): 0 
Gene Names: MRPL42MRPL31MRPS32RPML31HSPC204PTD007
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Entity ID: 36
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39S ribosomal protein L43, mitochondrialb148Homo sapiensMutation(s): 0 
Gene Names: MRPL43
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L44, mitochondrialc286Homo sapiensMutation(s): 0 
Gene Names: MRPL44
EC: 3.1.26
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Entity ID: 38
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39S ribosomal protein L45, mitochondriald171Homo sapiensMutation(s): 0 
Gene Names: MRPL45
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Entity ID: 39
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39S ribosomal protein L46, mitochondriale237Homo sapiensMutation(s): 0 
Gene Names: MRPL46C15orf4LIECG2
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Entity ID: 40
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39S ribosomal protein L48, mitochondrialf146Homo sapiensMutation(s): 0 
Gene Names: MRPL48CGI-118HSPC290
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Entity ID: 41
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39S ribosomal protein L49, mitochondrialg129Homo sapiensMutation(s): 0 
Gene Names: MRPL49C11orf4NOF1OK/SW-cl.67
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L50, mitochondrialh103Homo sapiensMutation(s): 0 
Gene Names: MRPL50
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Entity ID: 43
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39S ribosomal protein L51, mitochondriali97Homo sapiensMutation(s): 0 
Gene Names: MRPL51MRP64CDA09HSPC241
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Entity ID: 44
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39S ribosomal protein L52, mitochondrialj85Homo sapiensMutation(s): 0 
Gene Names: MRPL52
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Entity ID: 45
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39S ribosomal protein L53, mitochondrialk84Homo sapiensMutation(s): 0 
Gene Names: MRPL53
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Entity ID: 46
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39S ribosomal protein L54, mitochondriall23Homo sapiensMutation(s): 0 
Gene Names: MRPL54
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Entity ID: 47
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39S ribosomal protein L55, mitochondrialm45Homo sapiensMutation(s): 0 
Gene Names: MRPL55UNQ5835/PRO19675
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Entity ID: 49
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Peptidyl-tRNA hydrolase ICT1, mitochondrialp156Homo 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 1q128Homo sapiensMutation(s): 0 
Gene Names: GADD45GIP1MRPL59PLINP1PRG6
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Entity ID: 53
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Unknown protein/protein extensiont28Homo sapiensMutation(s): 0 
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Entity ID: 55
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Ribosome-recycling factor, mitochondrialz204Homo sapiensMutation(s): 0 
Gene Names: MRRF
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Entity ID: 58
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28S ribosomal protein S24, mitochondrialAC132Homo sapiensMutation(s): 0 
Gene Names: MRPS24HSPC335
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Entity ID: 59
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28S ribosomal protein S5, mitochondrialAD343Homo sapiensMutation(s): 0 
Gene Names: MRPS5
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Entity ID: 60
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28S ribosomal protein S6, mitochondrialAE122Homo sapiensMutation(s): 0 
Gene Names: MRPS6C21orf101RPMS6
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Entity ID: 61
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28S ribosomal protein S7, mitochondrialAF208Homo sapiensMutation(s): 0 
Gene Names: MRPS7
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Entity ID: 62
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28S ribosomal protein S9, mitochondrialAG326Homo sapiensMutation(s): 0 
Gene Names: MRPS9RPMS9
Find proteins for P82933 (Homo sapiens)
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PHAROS  P82933
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S10, mitochondrialAH122Homo sapiensMutation(s): 0 
Gene Names: MRPS10MSTP040
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PHAROS  P82664
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Entity ID: 64
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28S ribosomal protein S11, mitochondrialAI136Homo sapiensMutation(s): 0 
Gene Names: MRPS11RPMS11HCC2
Find proteins for P82912 (Homo sapiens)
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PHAROS  P82912
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Entity ID: 65
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28S ribosomal protein S12, mitochondrialAJ108Homo sapiensMutation(s): 0 
Gene Names: MRPS12RPMS12RPSM12
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PHAROS  O15235
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Entity ID: 67
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28S ribosomal protein S15, mitochondrialAL164Homo sapiensMutation(s): 0 
Gene Names: MRPS15RPMS15DC37
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PHAROS  P82914
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Entity ID: 68
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28S ribosomal protein S16, mitochondrialAM116Homo sapiensMutation(s): 0 
Gene Names: MRPS16RPMS16CGI-132
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PHAROS  Q9Y3D3
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Entity ID: 69
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28S ribosomal protein S17, mitochondrialAN107Homo sapiensMutation(s): 0 
Gene Names: MRPS17RPMS17HSPC011
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Entity ID: 70
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28S ribosomal protein S18b, mitochondrialAO185Homo sapiensMutation(s): 0 
Gene Names: MRPS18BC6orf14HSPC183PTD017
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PHAROS  Q9Y676
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Entity ID: 71
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28S ribosomal protein S18c, mitochondrialAP96Homo sapiensMutation(s): 0 
Gene Names: MRPS18CCGI-134
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PHAROS  Q9Y3D5
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Entity ID: 72
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28S ribosomal protein S21, mitochondrialAQ86Homo sapiensMutation(s): 0 
Gene Names: MRPS21RPMS21MDS016
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PHAROS  P82921
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Entity ID: 73
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28S ribosomal protein S22, mitochondrialAR242Homo sapiensMutation(s): 0 
Gene Names: MRPS22C3orf5RPMS22GK002
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PHAROS  P82650
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Entity ID: 75
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28S ribosomal protein S25, mitochondrialAT162Homo sapiensMutation(s): 0 
Gene Names: MRPS25RPMS25
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PHAROS  P82663
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Entity ID: 76
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28S ribosomal protein S26, mitochondrialAU173Homo sapiensMutation(s): 0 
Gene Names: MRPS26C20orf193RPMS13
Find proteins for Q9BYN8 (Homo sapiens)
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PHAROS  Q9BYN8
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
28S ribosomal protein S27, mitochondrialAV365Homo sapiensMutation(s): 0 
Gene Names: MRPS27KIAA0264
Find proteins for Q92552 (Homo sapiens)
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PHAROS  Q92552
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Entity ID: 78
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28S ribosomal protein S28, mitochondrialAW97Homo sapiensMutation(s): 0 
Gene Names: MRPS28MRPS35HSPC007
Find proteins for Q9Y2Q9 (Homo sapiens)
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PHAROS  Q9Y2Q9
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Entity ID: 79
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28S ribosomal protein S29, mitochondrialAX348Homo sapiensMutation(s): 0 
Gene Names: DAP3MRPS29
Find proteins for P51398 (Homo sapiens)
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PHAROS  P51398
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Entity ID: 80
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28S ribosomal protein S31, mitochondrialAY108Homo sapiensMutation(s): 0 
Gene Names: MRPS31IMOGN38
Find proteins for Q92665 (Homo sapiens)
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PHAROS  Q92665
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Entity ID: 81
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28S ribosomal protein S33, mitochondrialAZ87Homo sapiensMutation(s): 0 
Gene Names: MRPS33CGI-139PTD003
Find proteins for Q9Y291 (Homo sapiens)
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PHAROS  Q9Y291
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Entity ID: 82
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28S ribosomal protein S34, mitochondrialA0208Homo sapiensMutation(s): 0 
Gene Names: MRPS34
Find proteins for P82930 (Homo sapiens)
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PHAROS  P82930
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Entity ID: 83
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28S ribosomal protein S35, mitochondrialA1272Homo sapiensMutation(s): 0 
Gene Names: MRPS35MRPS28HDCMD11PMDS023PSEC0213
Find proteins for P82673 (Homo sapiens)
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PHAROS  P82673
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Entity ID: 84
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Coiled-coil-helix-coiled-coil-helix domain-containing protein 1A2116Homo sapiensMutation(s): 0 
Gene Names: CHCHD1C10orf34MRPS37
Find proteins for Q96BP2 (Homo sapiens)
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PHAROS  Q96BP2
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Entity ID: 85
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Aurora kinase A-interacting proteinA369Homo sapiensMutation(s): 0 
Gene Names: AURKAIP1AIPAKIPMRPS38
Find proteins for Q9NWT8 (Homo sapiens)
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PHAROS  Q9NWT8
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Entity ID: 86
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Pentatricopeptide repeat domain-containing protein 3, mitochondrialA4474Homo sapiensMutation(s): 0 
Gene Names: PTCD3
Find proteins for Q96EY7 (Homo sapiens)
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PHAROS  Q96EY7
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Entity ID: 18
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39S ribosomal protein L22, mitochondrialT166Homo sapiensMutation(s): 0 
Gene Names: MRPL22MRPL25RPML25HSPC158
Find proteins for Q9NWU5 (Homo sapiens)
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PHAROS  Q9NWU5
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Entity ID: 19
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39S ribosomal protein L23, mitochondrialU111Homo sapiensMutation(s): 0 
Gene Names: MRPL23L23MRPRPL23L
Find proteins for Q16540 (Homo sapiens)
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PHAROS  Q16540
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Entity ID: 22
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39S ribosomal protein L28, mitochondrialX243Homo sapiensMutation(s): 0 
Gene Names: MRPL28MAAT1
Find proteins for Q13084 (Homo sapiens)
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PHAROS  Q13084
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Entity ID: 24
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39S ribosomal protein L30, mitochondrialZ120Homo sapiensMutation(s): 0 
Gene Names: MRPL30MRPL28RPML28HSPC249
Find proteins for Q8TCC3 (Homo sapiens)
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PHAROS  Q8TCC3
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Entity ID: 3
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39S ribosomal protein L2, mitochondrialD236Homo sapiensMutation(s): 0 
Gene Names: MRPL2CGI-22
Find proteins for Q5T653 (Homo sapiens)
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PHAROS  Q5T653
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Entity ID: 33
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39S ribosomal protein L40, mitochondrial899Homo sapiensMutation(s): 0 
Gene Names: MRPL40NLVCFURIM
Find proteins for Q9NQ50 (Homo sapiens)
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PHAROS  Q9NQ50
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Entity ID: 34
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39S ribosomal protein L41, mitochondrial9123Homo sapiensMutation(s): 0 
Gene Names: MRPL41BMRPMRPL27RPML27PIG3
Find proteins for Q8IXM3 (Homo sapiens)
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PHAROS  Q8IXM3
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Entity ID: 48
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Ribosomal protein 63, mitochondrialo94Homo sapiensMutation(s): 0 
Gene Names: MRPL57MRP63
Find proteins for Q9BQC6 (Homo sapiens)
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PHAROS  Q9BQC6
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Entity ID: 51
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39S ribosomal protein S18a, mitochondrialr162Homo sapiensMutation(s): 0 
Gene Names: MRPS18A
Find proteins for Q9NVS2 (Homo sapiens)
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PHAROS  Q9NVS2
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Entity ID: 52
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39S ribosomal protein S30, mitochondrials390Homo sapiensMutation(s): 0 
Gene Names: MRPS30PDCD9BM-047
Find proteins for Q9NP92 (Homo sapiens)
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PHAROS  Q9NP92
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Entity ID: 57
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28S ribosomal protein S2, mitochondrialAB217Homo sapiensMutation(s): 0 
Gene Names: MRPS2CGI-91
Find proteins for Q9Y399 (Homo sapiens)
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PHAROS  Q9Y399
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Entity ID: 66
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28S ribosomal protein S14, mitochondrialAK101Homo sapiensMutation(s): 0 
Gene Names: MRPS14
Find proteins for O60783 (Homo sapiens)
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PHAROS  O60783
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Entity ID: 74
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28S ribosomal protein S23, mitochondrialAS126Homo sapiensMutation(s): 0 
Gene Names: MRPS23CGI-138HSPC329
Find proteins for Q9Y3D9 (Homo sapiens)
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PHAROS  Q9Y3D9
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1472Homo sapiens
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Entity ID: 2
MoleculeChainsLengthOrganismImage
mt-tRNAValB56Homo sapiens
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Entity ID: 56
MoleculeChainsLengthOrganismImage
12S rRNAAA923Homo sapiens
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  • Entity ID: 54
    MoleculeChainsLengthOrganismImage
    E-site tRNAu2Homo sapiens
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ZN
    Query on ZN

    Download CCD File 
    0, 4, AB, AO, AP, AT, r
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, AA, M, g
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 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
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM 32734

    Revision History 

    • Version 1.0: 2019-04-17
      Type: Initial release
    • Version 1.1: 2019-04-24
      Changes: Data collection, Database references
    • Version 1.2: 2019-05-08
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-11
      Changes: Author supporting evidence