PDBsum entry 2mst

RNA binding protein

PDB id: 2mst

Contents

Protein chain

75 a.a. *

* Residue conservation analysis

PDB id:

2mst

Name:

RNA binding protein

Title:

Musashi1 rbd2, nmr

Structure:

Protein (musashi1). Chain: a. Fragment: RNA-binding domain. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell: bl21(de3). Other_details: pcr

NMR struc:

20 models

Authors:

T.Nagata,R.Kanno,Y.Kurihara,S.Uesugi,T.Imai,S.Sakakibara,H.Okano, M.Katahira

Key ref:

T.Nagata et al. (1999). Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1. J Mol Biol, 287, 315-330. PubMed id: 10080895 DOI: 10.1006/jmbi.1999.2596

Date:

19-May-99 Release date: 19-May-00

Protein chain

Q61474  (MSI1H_MOUSE) -  RNA-binding protein Musashi homolog 1 from Mus musculus

Seq: 362 a.a.

Struc: 75 a.a.

DOI no: 10.1006/jmbi.1999.2596

J Mol Biol 287:315-330 (1999)

PubMed id: 10080895

Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1.

T.Nagata, R.Kanno, Y.Kurihara, S.Uesugi, T.Imai, S.Sakakibara, H.Okano, M.Katahira.

ABSTRACT

Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse central nervous system. Its restricted expression in neural precursor cells suggests that it is involved in the regulation of asymmetric cell division. Musashi1 contains two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), RBD1 and RBD2. Our previous studies showed that RBD1 alone binds to RNA, while the binding of RBD2 is not detected under the same conditions. Joining of RBD2 to RBD1, however, increases the affinity to greater than that of RBD1 alone, indicating that RBD2 contributes to RNA-binding. We have determined the three-dimensional solution structure of the C-terminal RBD (RBD2) of Musashi1 by NMR. It folds into a compact alpha beta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of RNP-type RBDs. Special structural features of RBD2 include a beta-bulge in beta2 and a shallow twist of the beta-sheet. The smaller 1H-15N nuclear Overhauser enhancement values for the residues of loop 3 between beta2 and beta3 suggest that this loop is flexible in the time-scale of nano- to picosecond order. The smaller 15N T2 values for the residues around the border between alpha2 and the following loop (loop 5) suggest this region undergoes conformational exchange in the milli- to microsecond time-scale. Chemical shift perturbation analysis indicated that RBD2 binds to an RNA oligomer obtained by in vitro selection under the conditions for NMR measurements, and thus the nature of the weak RNA-binding of RBD2 was successfully characterized by NMR, which is otherwise difficult to assess. Mainly the residues of the surface composed of the four-stranded beta-sheet, loops and C-terminal region are involved in the interaction. The appearance of side-chain NH proton resonances of arginine residues of loop 3 and imino proton resonances of RNA bases upon complex formation suggests the formation of intermolecular hydrogen bonds. The structural arrangement of the rings of the conserved aromatic residues of beta2 and beta3 is suitable for stacking interaction with RNA bases, known to be one of the major protein-RNA interactions, but a survey of the perturbation data suggested that the stacking interaction is not ideally achieved in the complex, which may be related to the weaker RNA-binding of RBD2.

Selected figure(s)

Figure 3.
Figure 3. The four-stranded antiparallel β-sheet of RBD2. Interstrand NOEs are indicated by double-headed continuous arrows, the NOEs with ambiguity due to overlapping being indicated by double-headed broken arrows. Slowly exchanging amide protons are indicated by bold H. Hydrogen bonds consistent with the NOEs and exchange data are indicated by broken lines. Black boxes on C^α indicate that the side-chains of these residues are presumed to point inside the protein.

Figure 4.
Figure 4. The structure of RBD2. (a) Superposition of the main-chains of 20 refined structures. N and C indicate K110 and A184, respectively, and loop 3 is labeled. (b) Schematic drawing of the restrained energy minimized mean structure derived from the 20 refined structures, as viewed from the same direction as that in (a). (c) Hydrophobic core. Overlaying of the 20 structures of the side-chains for residues involved in the hydrophobic core is shown on the main-chain of the restrained energy minimized mean structure. α-Helices and β-strands are colored red and sky-blue, respectively. (d) Hydrophobic patch exposed to the solvent. The same overlaying as that in (c) is shown for F112, F152 and F154, being rotated by ca 90 ° from that in (c).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 315-330) copyright 1999.

Figures were selected by an automated process.