PDBsum entry 5npm

RNA

PDB id: 5npm

Contents

Protein chain

211 a.a.

DNA/RNA

Ligands

MLI

Metals

_NA

Waters ×9

PDB id:

5npm

Name:

RNA

Title:

Crystal structure of mutant ribosomal protein tthl1 lacking 8 n- terminal residues in complex with 80nt 23s RNA from thermus thermophilus

Structure:

50s ribosomal protein l1. Chain: a. Engineered: yes. 23s ribosomal RNA. Chain: b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Gene: rpla, rpl1. Expressed in: escherichia coli. Expression_system_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.70Å R-factor: 0.204 R-free: 0.249

Authors:

A.G.Gabdulkhakov,T.V.Tishchenko,N.A.Nevskaya,S.V.Nikonov,M.B.Garber

Key ref:

O.S.Kostareva et al. (2018). [Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA]. Mol Biol (Mosk), 52, 106-111. PubMed id: 29512642 DOI: 10.7868/S0026898418010147

Date:

17-Apr-17 Release date: 16-May-18

Protein chain

Q5SLP7  (RL1_THET8) -  Large ribosomal subunit protein uL1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 229 a.a.

Struc: 211 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chain

G-G-G-A-U-G-C-G-U-A-G-G-A-U-A-G-G-U-G-G-G-A-G-C-C-U-G-U-G-A-A-C-C-C-C-C-G-C-C- 80 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.7868/S0026898418010147

Mol Biol (Mosk) 52:106-111 (2018)

PubMed id: 29512642

[Influence of Nonconserved Regions of L1 Protuberance of Thermus thermophilus Ribosome on the Affinity of L1 Protein to 23s rRNA].

O.S.Kostareva, N.A.Nevskaya, S.V.Tishchenko, A.G.Gabdulkhakov, M.B.Garber, S.V.Nikonov.

ABSTRACT

The L1 protuberance of the ribosome includes two domain ribosomal protein L1 and three helices of 23S rRNA (H76, H77, and H78) with interconnecting loops A and B. Helix 78 consists of two parts, i.e., H78a and H78b. A comparison of the available structural data of L1-RNA complexes with the obtained kinetic data made it possible to determine the influence of the nonconserved regions of Thermus thermophilus L1-protuberance on the mutual affinity of the L1 protein and 23S rRNA. It has been shown that the N-terminal helix of the protein and 78b helix of 23S rRNA are essential for the formation of an additional intermolecular contact, which is separated in the protein from the main site of L1-rRNA interaction by a flexible connection. This results in a rise in the TthL1-rRNA affinity. At the same time, the elongation of the 76 helix has no effect on rRNA-protein binding.