3iy8 | pdb_00003iy8

Leishmania tarentolae Mitonchondrial Ribosome small subunit

Loading... Status: waiting for Mol* initialization Structural highlights 3iy8 is a 11 chain structure with sequence from Escherichia coli and Leishmania tarentolae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RS11_ECOLI] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01310] [RS18_ECOUT] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [RS12_ECOLI] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [RS16_ECOLI] In addition to being a ribosomal protein, S16 also has a cation-dependent endonuclease activity. In-frame fusions with the ribosome maturation factor rimM suppress mutations in the latter (probably due to increased rimM expression) and are found in translationally active 70S ribosomes. [RS5_ECOLI] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp. [RS15_ECO57] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [RS8_ECOLI] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_01302_B] Protein S8 is a translational repressor protein, it controls the translation of the spc operon by binding to its mRNA.[HAMAP-Rule:MF_01302_B] [RS17_ECOLI] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. Also plays a role in translational accuracy; neamine-resistant ribosomes show reduced neamine-induced misreading in vitro.[HAMAP-Rule:MF_01345] [RS9_ECOLI] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. Mutations that decrease this affinity are suppressed in the 70S ribosome. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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). Structure of a mitochondrial ribosome with minimal RNA.,Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9637-42. Epub 2009 Jun 3. PMID:19497863 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosomal protein S11 Ribosomal protein S12 Ribosomal protein S15 Ribosomal protein S16 Ribosomal protein S17 Ribosomal protein S18 Ribosomal protein S8 Ribosomal protein S9

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