5aka | pdb_00005aka
EM structure of ribosome-SRP-FtsY complex in closed state
Structural highlights
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Function[RL29_ECOLI] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374] [RL16_ECOLI] This protein binds directly to 23S ribosomal RNA and is located at the A site of the peptidyltransferase center. It contacts the A and P site tRNAs. It has an essential role in subunit assembly, which is not well understood.[HAMAP-Rule:MF_01342] [RL21_ECOLI] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [RL11_ECOLI] This protein binds directly to 23S ribosomal RNA. Forms the L11 stalk, which is mobile in the ribosome, indicating its contribution to the activity of initiation, elongation and release factors.[HAMAP-Rule:MF_00736_B] [RL13_ECOLI] 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.[HAMAP-Rule:MF_01366] [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] [RL9_ECOLI] One of the primary rRNA binding proteins, it binds very close to the 3' end of the 23S rRNA.[HAMAP-Rule:MF_00503] [RL22_ECOLI] 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.[HAMAP-Rule:MF_01331_B] The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome where it lines the wall of the exit tunnel. Removal of most of this hairpin (residues 85-95) does not prevent its incorporation into 70S ribosomes. Two of the hairpin residues (91 and 93) seem to be involved in translation elongation arrest of the SecM protein, as their replacement by larger amino acids alleviates the arrest.[HAMAP-Rule:MF_01331_B] [RL20_ECOLI] One of the primary rRNA binding proteins, it binds close to the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_00382] [RL23_ECOLI] One of the early assembly proteins, it binds 23S rRNA; is essential for growth. One of the proteins that surround the polypeptide exit tunnel on the outside of the subunit. Acts as the docking site for trigger factor (PubMed:12226666) for Ffh binding to the ribosome (SRP54, PubMed:12756233 and PubMed:12702815) and to nascent polypeptide chains (PubMed:12756233).[HAMAP-Rule:MF_01369] [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] [RL5_ECOLI] 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. Its 5S rRNA binding is significantly enhanced in the presence of L18.[HAMAP-Rule:MF_01333_B] In the 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; the protein-protein contacts between S13 and L5 in B1b change in the model with bound EF-G implicating this bridge in subunit movement (PubMed:12809609 and PubMed:18723842). In the two 3.5 A resolved ribosome structures (PubMed:16272117) the contacts between L5, S13 and S19 are different, confirming the dynamic nature of this interaction.[HAMAP-Rule:MF_01333_B] Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [RL19_ECOLI] This protein is located at the 30S-50S ribosomal subunit interface. In the 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit forming part of bridges B6 and B8. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA. The protein conformation is quite different between the 50S and 70S structures, which may be necessary for translocation.[HAMAP-Rule:MF_00402] [RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B] [RL17_ECOLI] Requires L15 for assembly into the 50S subunit.[HAMAP-Rule:MF_01368] [RL4_ECOLI] 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.[1] Protein L4 is a both a transcriptional repressor and a translational repressor protein; these two functions are independent of each other. It regulates transcription of the S10 operon (to which L4 belongs) by causing premature termination of transcription within the S10 leader; termination absolutely requires the NusA protein. L4 controls the translation of the S10 operon by binding to its mRNA. The regions of L4 that control regulation (residues 131-210) are different from those required for ribosome assembly (residues 89-103).[2] Forms part of the polypeptide exit tunnel.[3] Can regulate expression from Citrobacter freundii, Haemophilus influenzae, Morganella morganii, Salmonella typhimurium, Serratia marcescens, Vibrio cholerae and Yersinia enterocolitica (but not Pseudomonas aeruginosa) S10 leaders in vitro.[4] [RL18_ECOLI] This is one of the proteins that mediates the attachment of the 5S rRNA subcomplex onto the large ribosomal subunit where it forms part of the central protuberance. Binds stably to 5S rRNA; increases binding abilities of L5 in a cooperative fashion; both proteins together confer 23S rRNA binding. The 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[5] [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.[6] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[7] [SRP54_ECOLI] Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY. Interaction with FtsY leads to the transfer of the RNC complex to the Sec translocase for insertion into the membrane, the hydrolysis of GTP by both Ffh and FtsY, and the dissociation of the SRP-FtsY complex into the individual components.[8] [9] [10] [11] [12] [13] [14] [RL3_ECOLI] One of two assembly inititator proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325_B] [RL6_ECOLI] This protein binds directly to at least 2 domains of the 23S ribosomal RNA, thus 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.[HAMAP-Rule:MF_01365] Gentamicin-resistant mutations in this protein affect translation fidelity.[HAMAP-Rule:MF_01365] [RL31_ECOLI] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [RL14_ECOLI] This protein binds directly to 23S ribosomal RNA. In the E.coli 70S ribosome (PubMed:12809609) it has been modeled to make two contacts with the 16S rRNA of the 30S subunit, forming part of bridges B5 and B8, connecting the 2 subunits. Although the protein undergoes significant rotation during the transition from an initiation to and EF-G bound state, the bridges remain stable. In the 3.5 A resolved structures (PubMed:16272117) L14 and L19 interact and together make contact with the 16S rRNA in bridges B5 and B8.[15] Can also interact with RsfA, in this case bridge B8 probably cannot form, and the 30S and 50S ribosomal subunits do not associate, which represses translation.[16] Publication Abstract from PubMedThe signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome-nascent chain complexes with signal sequences and undergo a series of distinct conformational changes, which ensures accurate timing and fidelity of protein targeting. Initial recruitment of the SRP receptor FtsY to the SRP-RNC complex results in GTP-independent binding of the SRP-FtsY GTPases at the SRP RNA tetraloop. In the presence of GTP, a closed state is adopted by the SRP-FtsY complex. The cryo-EM structure of the closed state reveals an ordered SRP RNA and SRP M domain with a signal sequence-bound. Van der Waals interactions between the finger loop and ribosomal protein L24 lead to a constricted signal sequence-binding pocket possibly preventing premature release of the signal sequence. Conserved M-domain residues contact ribosomal RNA helices 24 and 59. The SRP-FtsY GTPases are detached from the RNA tetraloop and flexible, thus liberating the ribosomal exit site for binding of the translocation machinery. Ribosome-SRP-FtsY cotranslational targeting complex in the closed state.,von Loeffelholz O, Jiang Q, Ariosa A, Karuppasamy M, Huard K, Berger I, Shan SO, Schaffitzel C Proc Natl Acad Sci U S A. 2015 Mar 16. pii: 201424453. PMID:25775537[17] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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