5wf0 | pdb_00005wf0
70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C2)
Structural highlights
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Function[RL31_ECO45] Binds the 23S rRNA. [RL10_ECO45] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [RL24_ECO55] 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. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [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. [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. [RL21_ECO45] This protein binds to 23S rRNA in the presence of protein L20. [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. [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. [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. [RL23_ECO57] 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. [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. [RL14_ECO45] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [RS20_ECO45] Binds directly to 16S ribosomal RNA. [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. [RL25_ECO55] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. [RS13_ECO57] 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 it has been 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. Contacts the tRNAs in the A and P sites (By similarity). [RL16_ECO45] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site 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. [RS17_ECO45] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RS6_ECOLU] Binds together with S18 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. [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. [RL11_ECO45] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. [EFTU2_ECO24] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [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. [RL15_ECOHS] Binds to the 23S rRNA. [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. [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. [RS19_ECO45] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS5_ECO57] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. [RL9_ECO45] Binds to the 23S rRNA. [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. [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] [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. [RS10_ECO45] Involved in the binding of tRNA to the ribosomes. [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. [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. Publication Abstract from PubMedThe GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.,Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J Nucleic Acids Res. 2018 May 4. pii: 4992653. doi: 10.1093/nar/gky346. PMID:29733411[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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