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.USA 106: 9637-9642

  • DOI: 10.1073/pnas.0901631106
  • Primary Citation of Related Structures:  

  • 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 e ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L2, mitochondrial
B
136Bos taurusMutation(s): 0 
Gene Names: MRPL2
Find proteins for Q2TA12 (Bos taurus)
Go to Gene View: MRPL2
Go to UniProtKB:  Q2TA12
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
C
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L4, mitochondrial
D
175N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
60N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L11, mitochondrial
G
145Bos taurusMutation(s): 0 
Gene Names: MRPL11
Find proteins for Q2YDI0 (Bos taurus)
Go to Gene View: MRPL11
Go to UniProtKB:  Q2YDI0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
140Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
121Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L16, mitochondrial
I
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L17, mitochondrial
S
116Bos taurusMutation(s): 0 
Gene Names: MRPL17
Find proteins for Q3T0L3 (Bos taurus)
Go to Gene View: MRPL17
Go to UniProtKB:  Q3T0L3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L22, mitochondrial
M
110Bos taurusMutation(s): 0 
Gene Names: MRPL22
Find proteins for Q3SZX5 (Bos taurus)
Go to Gene View: MRPL22
Go to UniProtKB:  Q3SZX5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
99Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L24, mitochondrial
N
96Bos taurusMutation(s): 0 
Gene Names: MRPL24
Find proteins for Q3SYS0 (Bos taurus)
Go to Gene View: MRPL24
Go to UniProtKB:  Q3SYS0
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L27, mitochondrial
O
69N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
X
63N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Y
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L33, mitochondrial
P
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
Leishmania Tarentolae Mitochondrial Large Ribosomal SubunitA1027Leishmania tarentolae
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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