5v8i | pdb_00005v8i

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Thermus thermophilus 70S ribosome lacking ribosomal protein uS17

spinqualitylabelsall models 5v8i, resolution 3.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5v8i is a 104 chain structure with sequence from Thet2 and Thermus thermophilus hb27. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ARG, MG, MPD, SF4, ZN NonStd Res: 0TD, 2MA, 2MG, 4OC, 5MC, 5MU, G7M, M2G, MA6, OMC, OMG, OMU, PSU, UR3 Gene: raiA, yfiA, b2597, JW2578 (THET2) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Warning: this is a large structure, and loading might take a long time or not happen at all. Function [RS2_THET2] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [RL25_THET2] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance (By similarity). [RL6_THET2] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). [RL31_THET2] Binds the 23S rRNA (By similarity). [RL21_THET2] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [RL22_THET2] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity). [RL20_THET2] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity). [RS13_THET2] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [RL32_THET2] Found on the solvent side of the large subunit (By similarity). [RS9_THET2] 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 (By similarity). [RL24_THET2] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity). [RL18_THET2] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance (By similarity). [RS19_THET2] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [RL14_THET2] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [RS4_THET2] 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 (By similarity). [RL15_THET2] Binds to the 23S rRNA (By similarity). [RS18_THET2] 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). [RS11_THET2] 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 (By similarity). [RS15_THET2] 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). [RL34_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [RL5_THET2] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity). [RS20_THET2] Binds directly to 16S ribosomal RNA (By similarity). [RS8_THET2] 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). [RS5_THET2] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity). [RL2_THET2] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity). [RSHX_THET2] 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 (By similarity). [RL13_THET2] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity). [RS10_THET2] Involved in the binding of tRNA to the ribosomes (By similarity). [RL16_THET2] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs (By similarity). [RS16_THET2] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [RL19_THET2] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site (By similarity). [RAIA_ECOLI] During stationary phase, prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases. In addition, during environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation initiation and increase translation accuracy. When normal growth conditions are restored, is quickly released from the ribosome. Inhibits translation initiation by blocking the A-site (aminoacyl-tRNA site) and P-site (peptidyl-tRNA site) of the ribosome. Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations. Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of RaiA in vivo. [RS7_THET2] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA (By similarity). [RL9_THET2] Binds to the 23S rRNA (By similarity). [RL3_THET2] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). [RS3_THET2] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [RS14Z_THET2] Binds 16S rRNA, 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). [RS6_THET2] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [RL23_THET2] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity). [RL4_THET8] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01328_B] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328_B] This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.[HAMAP-Rule:MF_01328_B]

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