5wnp

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

spinqualitylabelsall models 5wnp, resolution 3.30Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5wnp is a 23 chain structure with sequence from Thet8 and Thermus thermophilus (strain hb8 / atcc 27634 / dsm 579). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: K, MG, ZN NonStd Res: 0TD, 12A, 2MG, 4OC, 5MC, 70U, 7MG, M2G, MA6, PSU, UR3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RS11_THET8] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [RSHX_THET8] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [RS7_THET8] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [RS17_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345] Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [RS18_THET8] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [RS16_THET8] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [RS13_THET8] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [RS6_THET8] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [RS3_THET8] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [RS9_THET8] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [RS12_THET8] With S4 and S5 plays an important role in translational accuracy (By similarity).[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.[HAMAP-Rule:MF_00403_B] [RS20_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [RS14Z_THET8] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [RS15_THET8] 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).[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [RS8_THET8] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [RS4_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [RS19_THET8] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [RS10_THET8] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [RS5_THET8] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B] Publication Abstract from PubMed Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation. 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.,Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD Nat Struct Mol Biol. 2018 Mar;25(3):208-216. doi: 10.1038/s41594-018-0030-z. Epub, 2018 Feb 19. PMID:29459784 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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