PDBsum entry 2r1c

RNA binding protein

PDB id: 2r1c

Contents

Protein chain

91 a.a. *

* Residue conservation analysis

PDB id:

2r1c

Name:

RNA binding protein

Title:

Coordinates of the thermus thermophilus ribosome binding factor a (rbfa) homology model as fitted into the cryo-em map of a 30s-rbfa complex

Structure:

Ribosome-binding factor a. Chain: a. Synonym: rbfa, ttha0907. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ttha0907. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Authors:

P.P.Datta,D.N.Wilson,M.Kawazoe,N.K.Swami,T.Kaminishi,M.R.Sharma, T.M.Booth,C.Takemoto,P.Fucini,S.Yokoyama,R.K.Agrawal

Key ref:

P.P.Datta et al. (2007). Structural aspects of RbfA action during small ribosomal subunit assembly. Mol Cell, 28, 434-445. PubMed id: 17996707 DOI: 10.1016/j.molcel.2007.08.026

Date:

22-Aug-07 Release date: 18-Mar-08

Protein chain

Q5SJV1  (RBFA_THET8) -  Ribosome-binding factor A from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 95 a.a.

Struc: 91 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.molcel.2007.08.026

Mol Cell 28:434-445 (2007)

PubMed id: 17996707

Structural aspects of RbfA action during small ribosomal subunit assembly.

P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, R.K.Agrawal.

ABSTRACT

Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.

Selected figure(s)

Figure 1.
Figure 1. Crystal Structure of Tth RbfA and Its Comparison with Known Atomic Structures of RbfA from Other Species
(A) Stereo representation of the Tth RbfA is shown in cartoon (PDB ID, 2DYJ).
(B) An enlarged view of the helix-kink-helix motif (cyan) with all residues in stick. Residues involved in notable interactions, Asp25 and Arg27 on the 3[10] helix (magenta) and the conserved Phe87, are also shown in stick.
(C) Stereo representation of Tth RbfA in the surface potential prepared by using APBS tools built in PyMOL.
(D) Superposition of structures of RbfA from T. Thermophilus (molecules A and B in the asymmetric unit are shown in dark and light blue colors, respectively), H. influenzae (green, 1JOS), and M. pneumoniae (orange, 1PA4). In all panels, N, C, and hkh mean N terminus, C terminus, and helix-kink-helix motif, respectively.

Figure 7.
Figure 7. Comparison of the Binding Positions of RbfA and Era on the 30S Subunit
(A) Binding position of RbfA (red) and Era (magenta; Sharma et al., 2005) on the 30S subunit.
(B) RbfA (red) and Era (magenta) interact with a common structural element, h28, of the 16S rRNA (cyan). The thumbnail to the left depicts the orientation of the 30S subunit.

The above figures are reprinted from an Open Access publication published by Cell Press: Mol Cell (2007, 28, 434-445) copyright 2007.

Figures were selected by an automated process.