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 1.3 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: https://doi.org/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. 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).


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L2, mitochondrial136Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q2TA12 (Bos taurus)
Explore Q2TA12 
Go to UniProtKB:  Q2TA12
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TA12
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3209Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
Explore P60438 
Go to UniProtKB:  P60438
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60438
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L4, mitochondrial175Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYD3 (Homo sapiens)
Explore Q9BYD3 
Go to UniProtKB:  Q9BYD3
PHAROS:  Q9BYD3
GTEx:  ENSG00000105364 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYD3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9E [auth H]60Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Explore P0A7R1 
Go to UniProtKB:  P0A7R1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7R1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L11, mitochondrialF [auth G]145Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q2YDI0 (Bos taurus)
Explore Q2YDI0 
Go to UniProtKB:  Q2YDI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2YDI0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth J]140Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
Explore P0AA10 
Go to UniProtKB:  P0AA10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AA10
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth K]121Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Explore P0ADY3 
Go to UniProtKB:  P0ADY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADY3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15I [auth L]144Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
Explore P02413 
Go to UniProtKB:  P02413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02413
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L16, mitochondrialJ [auth I]118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX20 (Homo sapiens)
Explore Q9NX20 
Go to UniProtKB:  Q9NX20
PHAROS:  Q9NX20
GTEx:  ENSG00000166902 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX20
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L17, mitochondrialK [auth S]116Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q3T0L3 (Bos taurus)
Explore Q3T0L3 
Go to UniProtKB:  Q3T0L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3T0L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20L [auth Q]117Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Explore P0A7L3 
Go to UniProtKB:  P0A7L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7L3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21M [auth R]103Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
Explore P0AG48 
Go to UniProtKB:  P0AG48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L22, mitochondrialN [auth M]110Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q3SZX5 (Bos taurus)
Explore Q3SZX5 
Go to UniProtKB:  Q3SZX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SZX5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23O [auth T]99Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Explore P0ADZ0 
Go to UniProtKB:  P0ADZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L24, mitochondrialP [auth N]96Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q3SYS0 (Bos taurus)
Explore Q3SYS0 
Go to UniProtKB:  Q3SYS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SYS0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L27, mitochondrialQ [auth O]69Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0M9 (Homo sapiens)
Explore Q9P0M9 
Go to UniProtKB:  Q9P0M9
PHAROS:  Q9P0M9
GTEx:  ENSG00000108826 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0M9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29R [auth X]63Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Explore P0A7M6 
Go to UniProtKB:  P0A7M6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7M6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30S [auth Y]58Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
Explore P0AG51 
Go to UniProtKB:  P0AG51
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AG51
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
39S ribosomal protein L33, mitochondrialT [auth P]52Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75394 (Homo sapiens)
Explore O75394 
Go to UniProtKB:  O75394
PHAROS:  O75394
GTEx:  ENSG00000243147 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75394
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit1,027Leishmania tarentolae
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references