PDBsum entry 2ftc

Ribosome

PDB id: 2ftc

Contents

Protein chains

189 a.a.* *

136 a.a.* *

211 a.a.* *

175 a.a.* *

137 a.a.* *

145 a.a.* *

148 a.a.* *

118 a.a.* *

116 a.a.* *

98 a.a.* *

118 a.a.* *

110 a.a.* *

96 a.a.* *

69 a.a.* *

52 a.a.* *

38 a.a.* *

DNA/RNA

* Residue conservation analysis

* C-alpha coords only

PDB id:

2ftc

Name:

Ribosome

Title:

Structural model for the large subunit of the mammalian mitochondrial ribosome

Structure:

Mitochondrial 16s ribosomal RNA. Chain: r. Mitochondrial ribosomal protein l1. Chain: a. Mitochondrial ribosomal protein l2. Chain: b. Mitochondrial 39s ribosomal protein l3. Chain: c. Synonym: l3mt, mrp-l3.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Bovine,cow,domestic cattle,domestic cow. Organism_taxid: 9913

Biol. unit:

80mer (from PQS)

Authors:

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

Key ref:

J.A.Mears et al. (2006). A structural model for the large subunit of the mammalian mitochondrial ribosome. J Mol Biol, 358, 193-212. PubMed id: 16510155 DOI: 10.1016/j.jmb.2006.01.094

Date:

24-Jan-06 Release date: 11-Apr-06

Protein chain

A6QPQ5  (RM01_BOVIN) -  Large ribosomal subunit protein uL1m from Bos taurus

Seq: 325 a.a.

Struc: 189 a.a.*

Protein chain

Q2TA12  (RM02_BOVIN) -  Large ribosomal subunit protein uL2m from Bos taurus

Seq: 306 a.a.

Struc: 136 a.a.*

Protein chain

Q3ZBX6  (RM03_BOVIN) -  Large ribosomal subunit protein uL3m from Bos taurus

Seq: 348 a.a.

Struc: 211 a.a.*

Protein chain

Q32PI6  (RM04_BOVIN) -  Large ribosomal subunit protein uL4m from Bos taurus

Seq: 294 a.a.

Struc: 175 a.a.*

Protein chains

Q7YR75  (RM12_BOVIN) -  Large ribosomal subunit protein bL12m from Bos taurus

Seq: 198 a.a.

Struc: 137 a.a.

Protein chain

Q2YDI0  (RM11_BOVIN) -  Large ribosomal subunit protein uL11m from Bos taurus

Seq: 192 a.a.

Struc: 145 a.a.*

Protein chain

Q3SYS1  (RM13_BOVIN) -  Large ribosomal subunit protein uL13m from Bos taurus

Seq: 178 a.a.

Struc: 148 a.a.*

Protein chain

Q3T0J3  (RM16_BOVIN) -  Large ribosomal subunit protein uL16m from Bos taurus

Seq: 251 a.a.

Struc: 118 a.a.*

Protein chain

Q3T0L3  (RM17_BOVIN) -  Large ribosomal subunit protein bL17m from Bos taurus

Seq: 172 a.a.

Struc: 116 a.a.*

Protein chain

Q2HJI0  (RM19_BOVIN) -  Large ribosomal subunit protein bL19m from Bos taurus

Seq: 292 a.a.

Struc: 98 a.a.*

Protein chain

Q2TBR2  (RM20_BOVIN) -  Large ribosomal subunit protein bL20m from Bos taurus

Seq: 149 a.a.

Struc: 118 a.a.*

Protein chain

Q3SZX5  (RM22_BOVIN) -  Large ribosomal subunit protein uL22m from Bos taurus

Seq: 204 a.a.

Struc: 110 a.a.*

Protein chain

Q3SYS0  (RM24_BOVIN) -  Large ribosomal subunit protein uL24m from Bos taurus

Seq: 216 a.a.

Struc: 96 a.a.*

Protein chain

Q32PC3  (RM27_BOVIN) -  Large ribosomal subunit protein bL27m from Bos taurus

Seq: 148 a.a.

Struc: 69 a.a.*

Protein chain

Q3SZ47  (RM33_BOVIN) -  Large ribosomal subunit protein bL33m from Bos taurus

Seq: 65 a.a.

Struc: 52 a.a.*

Protein chain

A8NN94  (RM34_BOVIN) -  Large ribosomal subunit protein bL34m from Bos taurus

Seq: 96 a.a.

Struc: 38 a.a.*

* PDB and UniProt seqs differ at 178 residue positions (black crosses)

DNA/RNA chain

A-C-U-A-G-A-C-C-U-A-G-C-C-C-A-A-A-A-G-U-A-U-A-G-G-A-G-A-U-A-G-A-A-A-U-C-G-G-C- ... 1443 bases

reference

DOI no: 10.1016/j.jmb.2006.01.094

J Mol Biol 358:193-212 (2006)

PubMed id: 16510155

A structural model for the large subunit of the mammalian mitochondrial ribosome.

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

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 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.

Selected figure(s)

Figure 5.
Figure 5. Three-dimensional model for the mitochondrial 16 S rRNA. (a) The 16 S rRNA is represented from the interface and solvent-accessible sides of the structure and colored by domain (I, purple; II, dark blue; III, orange; IV, green; V, red; and VI, yellow). (b) The model RNA fit to EM density that is attributable to RNA,13 except for the tip of a domain V helix that contacts the L1 protein. However, the model of the extended rRNA segment fits into the complete LSU map (also see Figure 4(b)). Coloring is the same as in (a).

Figure 7.
Figure 7. Stereo-view representation of the 3D model of the 39 S subunit of the mitochondrial ribosome. (a) The interface view of the subunit shows that the conserved interface of the mitochondrial ribosome is still dominated by rRNA structure (colored as in Figure 5). (b) The homologous MRPs (grey) are located predominantly towards the solvent-accessible side of the particle. Upper and lower panels in both sections show the modeled structure (rRNA and proteins), and its fitting into the cryo-EM map,13 respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 193-212) copyright 2006.

Figures were selected by the author.