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4v9f

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The re-refined crystal structure of the Haloarcula marismortui large ribosomal subunit at 2.4 Angstrom resolution: more complete structure of the L7/L12 and L1 stalk, L5 and LX proteins

Structural highlights

4v9f is a 10 chain structure with sequence from Haloarcula marismortui ATCC 43049. This structure supersedes the now removed PDB entries 4hub and 4i4m. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.404Å
Ligands:	, , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL2_HALMA 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).[HAMAP-Rule:MF_01320_A]

Publication Abstract from PubMed

The structure of the large ribosomal subunit from the halophilic archaeon Haloarcula marismortui (Hma) is the only crystal structure of an archaeal ribosomal particle that has been determined to date. However, the first model of the Hma 50S ribosomal subunit contained some gaps: the structures of functionally important mobile lateral protuberances were not visualized. Subsequently, some parts of the P (L12) stalk base were visualized at 3.0 A resolution [Kavran & Steitz (2007), J. Mol. Biol. 371, 1047-1059]: the RNA-binding domain of r-protein P0 (L10), the C-terminal domain of L11 and helices 43 and 44 of the 23 S rRNA. Here, the 2.4 A resolution electron-density map of the Hma 50S ribosomal subunit was revisited and approximately two-thirds of the P0 protein, residues 1-58 of the N-terminal domains of two P1 protein molecules, residues 130-156 of L11, the full-length r-protein LX, nucleotides 2137-2149 and 2226-2237 of the 23S rRNA helix H76 forming the L1 stalk, nucleotides 2339-2343 of the 23S rRNA (contacting L5 protein) and loops 29-34 and 108-128 of protein L5 could be visualized. Thus, this paper provides a supplemented version of the Hma 50S ribosomal subunit model.

Revisiting the Haloarcula marismortui 50S ribosomal subunit model.,Gabdulkhakov A, Nikonov S, Garber M Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):997-1004. doi:, 10.1107/S0907444913004745. Epub 2013 May 11. PMID:23695244^[1]

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

References

↑ Gabdulkhakov A, Nikonov S, Garber M. Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr D Biol Crystallogr. 2013 Jun;69(Pt 6):997-1004. doi:, 10.1107/S0907444913004745. Epub 2013 May 11. PMID:23695244 doi:http://dx.doi.org/10.1107/S0907444913004745