PDBsum entry 2d3o

Ribosome

PDB id: 2d3o

Contents

Protein chains

93 a.a. *

110 a.a. *

66 a.a. *

100 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

2d3o

Name:

Ribosome

Title:

Structure of ribosome binding domain of the trigger factor on the 50s ribosomal subunit from d. Radiodurans

Structure:

23s ribosomal RNA. Chain: 0. 50s ribosomal protein l23. Chain: r. 50s ribosomal protein l24. Chain: s. 50s ribosomal protein l29. Chain: w. Trigger factor.

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Pentamer (from PQS)

Resolution:

3.35Å R-factor: 0.299 R-free: 0.322

Authors:

F.Schluenzen,D.N.Wilson,H.A.Hansen,P.Tian,J.M.Harms,S.J.Mcinnes, R.Albrecht,J.Buerger,S.M.Wilbanks,P.Fucini

Key ref:

F.Schlünzen et al. (2005). The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction. Structure (Camb), 13, 1685-1694. PubMed id: 16271892 DOI: 10.1016/j.str.2005.08.007

Date:

30-Sep-05 Release date: 06-Dec-05

Protein chain

Q9RXK0  (RL23_DEIRA) -  Large ribosomal subunit protein uL23 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 95 a.a.

Struc: 93 a.a.

Protein chain

Q9RXJ1  (RL24_DEIRA) -  Large ribosomal subunit protein uL24 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 115 a.a.

Struc: 110 a.a.

Protein chain

Q9RXJ4  (RL29_DEIRA) -  Large ribosomal subunit protein uL29 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 67 a.a.

Struc: 66 a.a.

Protein chain

Q9RT21  (TIG_DEIRA) -  Trigger factor from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 465 a.a.

Struc: 100 a.a.

DNA/RNA chain

G-G-U-C-A-A-G-A-U-A-G-U-A-A-G-G-G-U-C-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-G-C- ... 2802 bases

Enzyme reactions

• Enzyme class 1: Chain 1: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
• Enzyme class 2: Chains R, S, W: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.str.2005.08.007

Structure (Camb) 13:1685-1694 (2005)

PubMed id: 16271892

The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.

F.Schlünzen, D.N.Wilson, P.Tian, J.M.Harms, S.J.McInnes, H.A.Hansen, R.Albrecht, J.Buerger, S.M.Wilbanks, P.Fucini.

ABSTRACT

This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex. The beta hairpin loop of eubacterial L24, which is shorter in archaeal ribosomes, contacts the TF and severely diminishes the molecular cradle proposed to exist between the TF and ribosome. Bound to the ribosome, TF exposes a hydrophobic crevice large enough to accommodate the nascent polypeptide chain. Superimposition of the full-length TF and the signal-recognition particle (SRP) onto the complex shows that simultaneous cohabitation is possible, in agreement with biochemical data, and suggests a model for the interplay of TF, SRP, and the nascent chain during translation.

Selected figure(s)

Figure 5.
Figure 5. Model for Interplay between the TF, SRP, and the Nascent Chain during Translation
Schematic view of the bottom of the ribosome, showing ribosomal proteins L23, (green), L24 (yellow), and L29 (orange), and with the tunnel exit site indicated with an arrow. (A) TF is the first chaperone to bind to the bacterial ribosome as the nascent chain emerges from the tunnel. Direct contact between L24 and the TF results in conformational changes in the TF-BD that expose a hydrophobic crevice located in the TF-BD, through which the polypeptide chain can pass. (B) The SRP particle binds to the ribosome in the presence of the TF, initially through contacts with L29. The M domain of the SRP covers the hydrophobic cavity in the TF-BD and monitors for the presence of a signal sequence in the nascent chain. (C) Interaction between the signal sequence-containing nascent chain and the M domain of the SRP enables the M domain to establish contact with H24 of the 23S rRNA. This interaction stabilizes the SRP particle on the ribosome and could lead to dissociation of the TF. (D) In the absence of a signal sequence, the M domain cannot establish contact with the 23S rRNA, and the SRP dissociates from the ribosome. Continued translation leads to elongation of the nascent chain, which is channeled through the hydrophobic cavity into the central cavity (body) of the TF. The restricted size of the cavity due to the presence of L24 limits the possibility for folding of entire protein domains. The PPIase domain (head) of the TF may recognize the nascent chain as it emerges from the head side, monitoring for proline residues that need to be isomerized (arrowed).

The above figure is reprinted by permission from Cell Press: Structure (Camb) (2005, 13, 1685-1694) copyright 2005.

Figure was selected by an automated process.