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
  • Also Cited By: 3IY9

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L1
A
189Bos taurusGene Names: MRPL1
Find proteins for A6QPQ5 (Bos taurus)
Go to Gene View: MRPL1
Go to UniProtKB:  A6QPQ5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L2
B
136Bos taurusGene Names: MRPL2
Find proteins for Q2TA12 (Bos taurus)
Go to Gene View: MRPL2
Go to UniProtKB:  Q2TA12
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial 39S ribosomal protein L3
C
211Bos taurusGene Names: MRPL3
Find proteins for Q3ZBX6 (Bos taurus)
Go to Gene View: MRPL3
Go to UniProtKB:  Q3ZBX6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L4 isoform a
D
175Bos taurusGene Names: MRPL4
Find proteins for Q32PI6 (Bos taurus)
Go to Gene View: MRPL4
Go to UniProtKB:  Q32PI6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L12, mitochondrial
E, F
137Bos taurusGene Names: MRPL12
Find proteins for Q7YR75 (Bos taurus)
Go to Gene View: MRPL12
Go to UniProtKB:  Q7YR75
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L11, mitochondrial
G
145Bos taurusGene Names: MRPL11
Find proteins for Q2YDI0 (Bos taurus)
Go to Gene View: MRPL11
Go to UniProtKB:  Q2YDI0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L13, mitochondrial
H
148Bos taurusGene Names: MRPL13
Find proteins for Q3SYS1 (Bos taurus)
Go to Gene View: MRPL13
Go to UniProtKB:  Q3SYS1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L16
I
118Bos taurusGene Names: MRPL16
Find proteins for Q3T0J3 (Bos taurus)
Go to Gene View: MRPL16
Go to UniProtKB:  Q3T0J3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial ribosomal protein L17
J
116Bos taurusGene Names: MRPL17
Find proteins for Q3T0L3 (Bos taurus)
Go to Gene View: MRPL17
Go to UniProtKB:  Q3T0L3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L19, mitochondrial
K
98Bos taurusGene Names: MRPL19
Find proteins for Q2HJI0 (Bos taurus)
Go to Gene View: MRPL19
Go to UniProtKB:  Q2HJI0
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
MRPL20 protein
L
118Bos taurusGene Names: MRPL20
Find proteins for Q2TBR2 (Bos taurus)
Go to Gene View: MRPL20
Go to UniProtKB:  Q2TBR2
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L22 isoform a
M
110Bos taurusGene Names: MRPL22
Find proteins for Q3SZX5 (Bos taurus)
Go to Gene View: MRPL22
Go to UniProtKB:  Q3SZX5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L24
N
96Bos taurusGene Names: MRPL24
Find proteins for Q3SYS0 (Bos taurus)
Go to Gene View: MRPL24
Go to UniProtKB:  Q3SYS0
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial 39S ribosomal protein L27
O
69Bos taurusGene Names: MRPL27
Find proteins for Q32PC3 (Bos taurus)
Go to Gene View: MRPL27
Go to UniProtKB:  Q32PC3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
mitochondrial ribosomal protein L33 isoform a
P
52Bos taurusGene Names: MRPL33
Find proteins for Q3SZ47 (Bos taurus)
Go to Gene View: MRPL33
Go to UniProtKB:  Q3SZ47
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
39S ribosomal protein L34, mitochondrial
Q
38Bos taurusGene Names: MRPL34
Find proteins for A8NN94 (Bos taurus)
Go to Gene View: MRPL34
Go to UniProtKB:  A8NN94
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 
Software Package:
Software NamePurpose
YAMMPrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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