4kbw

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4kbw, resolution 3.86Å ()
Non-Standard Residues:
Related: 4kbt, 4kbu, 4kbv


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state. This entry contains 50S ribosomal subunit B. The full asymmetric unit also contains PDB entries 4KBV (30S subunit B), 4KBT (30S subunit A), and 4KBU (50S subunit A).

Publication Abstract from PubMed

Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with beta,gamma-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation., Zhou J, Lancaster L, Donohue JP, Noller HF, Science. 2013 Jun 28;340(6140):1236086. doi: 10.1126/science.1236086. PMID:23812722

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[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). [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). [RL1_THET2] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (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). [RL21_THET2] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [RL32_THET2] Found on the solvent side of the large subunit (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). [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). [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). [RL15_THET2] Binds to the 23S rRNA (By similarity). [RL16_THET2] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs (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). [RL31_THET2] Binds the 23S rRNA (By similarity). [RL34_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [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). [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). [RL14_THET2] Binds to 23S rRNA. Forms part of two intersubunit bridges in 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). [RL11_THET2] This protein binds directly to 23S ribosomal RNA (By similarity). [RL4_THET2] 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). Forms part of the polypeptide exit tunnel (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). [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).

About this Structure

4kbw is a 36 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA.

Reference

  • Zhou J, Lancaster L, Donohue JP, Noller HF. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science. 2013 Jun 28;340(6140):1236086. doi: 10.1126/science.1236086. PMID:23812722 doi:10.1126/science.1236086

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