2FTC

Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 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

A Structural Model for the Large Subunit of the Mammalian Mitochondrial Ribosome

Mears, J.A.Sharma, M.R.Gutell, R.R.McCook, A.S.Richardson, P.E.Caulfield, T.R.Agrawal, R.K.Harvey, S.C.

(2006) J Mol Biol 358: 193-212

  • DOI: 10.1016/j.jmb.2006.01.094
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different speci ...

    Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.


    Organizational Affiliation

    Department of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA.



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L17
J
116Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L19, mitochondrial
K
98Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
MRPL20 protein
L
118Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L22 isoform a
M
110Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L24
N
96Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial 39S ribosomal protein L27
O
69Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L33 isoform a
P
52Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L34, mitochondrial
Q
38Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L1
A
189Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L2
B
136Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial 39S ribosomal protein L3
C
211Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L4 isoform a
D
175Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L12, mitochondrial
E, F
137Bos taurusMutation(s): 0 
Gene Names: MRPL12
Find proteins for Q7YR75 (Bos taurus)
Go to UniProtKB:  Q7YR75

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L11, mitochondrial
G
145Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L13, mitochondrial
H
148Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L16
I
118Bos taurusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 1
MoleculeChainsLengthOrganism
Mitochondrial 16S ribosomal RNAR1568Bos taurus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance