6dnc

E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codonE.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon

6dnc, resolution 3.70Å Show:Asymmetric Unit Biological Assembly Structural highlights 6dnc is a 59 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895 and Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Gene: prfA, ECS88_1279 ("Bacillus coli" Migula 1895) Experimental data: Check Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [RL20_ECO45] 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. [RL3_ECO45] 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. [RL25_ECOLI] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336] [RL16_ECO45] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [RL15_ECOLI] This protein binds the 5S rRNA. It is required for the late stages of subunit assembly, and is essential for 5S rRNA assembly onto the ribosome.[HAMAP-Rule:MF_01341_B] [RS7_ECO45] 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. [RS18_ECO45] 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. [RL24_ECOLI] 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. It is not thought to be involved in the functions of the mature 50S subunit in vitro. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [RS20_ECO45] Binds directly to 16S ribosomal RNA. [RS3_ECO45] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [RL13_ECO45] 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. [RL19_ECO45] 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. [RS12_ECO45] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] 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] [B7MCT3_ECO45] 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.[HAMAP-Rule:MF_01369] [RL6_ECO45] 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. [RL31_ECO45] Binds the 23S rRNA. [RL9_ECO45] Binds to the 23S rRNA. [RS11_ECO45] 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. [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. [RL21_ECO45] This protein binds to 23S rRNA in the presence of protein L20. [RL11_ECO45] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. [RL22_ECO45] 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. [RS13_ECOLI] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder. Contacts the tRNAs in the A and P sites. The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs. [RL5_ECO45] 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. [RS14_ECO45] 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. [RS4_ECO45] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [RL10_ECO45] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [RS10_ECO45] Involved in the binding of tRNA to the ribosomes. [RL14_ECO45] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [RL4_ECO45] 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. Forms part of the polypeptide exit tunnel. [RS15_ECO45] 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. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. [RF1_ECO45] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA. [RS19_ECO45] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS8_ECO45] 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. [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] [RL18_ECO45] 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. [RS17_ECO45] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RL1_ECO45] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release. Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA. Publication Abstract from PubMed Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the Escherichia coli 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile 196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1. Mechanism of premature translation termination on a sense codon.,Svidritskiy E, Demo G, Korostelev A J Biol Chem. 2018 Jun 25. pii: AW118.003232. doi: 10.1074/jbc.AW118.003232. PMID:29941456 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosome 3D structures