3IY9

Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.1 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

Structure of a mitochondrial ribosome with minimal RNA

Sharma, M.R.Booth, T.M.Simpson, L.Maslov, D.A.Agrawal, R.K.

(2009) Proc Natl Acad Sci U S A 106: 9637-9642

  • DOI: 10.1073/pnas.0901631106
  • Primary Citation of Related Structures:  
    3IY8, 3IY9

  • PubMed Abstract: 
  • The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge ...

    The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the alpha-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).


    Related Citations: 
    • Structures of the bacterial ribosome at 3.5 A resolution
      Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., Cate, J.H.D.
      (2005) Science 310: 827
    • A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome
      Mears, J.A., Sharma, M.R., Gutell, R.R., Richardson, P.E., Agrawal, R.K.
      (2006) J Mol Biol 358: 193

    Organizational Affiliation

    Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrialB136Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3C209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrialD175Homo sapiensMutation(s): 0 
Gene Names: MRPL4CDABP0091CGI-28
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9E [auth H]60Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialF [auth G]145Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]140Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 8
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50S ribosomal protein L14H [auth K]121Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 9
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50S ribosomal protein L15I [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialJ [auth I]118Homo sapiensMutation(s): 0 
Gene Names: MRPL16PNAS-111
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialK [auth S]116Homo sapiensMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L20L [auth Q]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 13
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50S ribosomal protein L21M [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 14
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39S ribosomal protein L22, mitochondrialN [auth M]110Homo sapiensMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L23O [auth T]99Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialP [auth N]96Homo sapiensMutation(s): 0 
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Entity ID: 17
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39S ribosomal protein L27, mitochondrialQ [auth O]69Homo sapiensMutation(s): 0 
Gene Names: MRPL27HSPC250
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Entity ID: 18
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50S ribosomal protein L29R [auth X]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 19
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50S ribosomal protein L30S [auth Y]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 20
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39S ribosomal protein L33, mitochondrialT [auth P]52Homo sapiensMutation(s): 0 
Gene Names: MRPL33C2orf1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Leishmania Tarentolae Mitochondrial Large Ribosomal SubunitA1027Leishmania tarentolae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Data collection