4kd8

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4kd8, resolution 3.50Å ()
Ligands: , ,
Non-Standard Residues: , , ,
Related: 4kd9, 4kda, 4kdb


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


Contents

70S Ribosome translocation intermediate FA-3.6A CONTAINING ELONGATION FACTOR EFG/FUSIDIC ACID/GDP, MRNA, AND TRNA BOUND IN THE pe*/E STATE. THIS ENTRY CONTAINS THE 30S RIBOSOMAL SUBUNIT A. THE 50S SUBUNIT A CAN BE FOUND IN 4KD9. MOLECULE B IN THE SAME ASYMMETRIC UNIT IS DEPOSITED AS 4KDA (30S) AND 4KDB (50S).

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

[RS12_THET2] With S4 and S5 plays an important role in translational accuracy (By similarity). 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 (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). [RS3_THET2] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (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). [RS2_THET2] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [RS19_THET2] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [EFG_THET2] Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome (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). [RS17_THET2] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [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). [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). [RS10_THET2] Involved in the binding of tRNA to the ribosomes (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). [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). [RS16_THET2] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (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). [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). [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). [RS20_THET2] Binds directly to 16S ribosomal RNA (By similarity). [RS6_THET2] Located on the outer edge of the platform on the body of the 30S subunit (By similarity).

About this Structure

4kd8 is a 24 chain structure with sequence from Escherichia coli, Streptomyces and Thermus thermophilus. Full crystallographic information is available from OCA.

See Also

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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