PDBsum entry 1hd0

RNA binding protein

PDB id: 1hd0

Contents

Protein chain

75 a.a. *

* Residue conservation analysis

PDB id:

1hd0

Name:

RNA binding protein

Title:

Heterogeneous nuclear ribonucleoprotein d0 (hnrnp d0 rbd1), nmr

Structure:

Protein (heterogeneous nuclear ribonucleoprotein d0). Chain: a. Fragment: RNA-binding domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Cell: hela. Cellular_location: nucleus. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_cell: bl21(de3). Other_details: pcr

NMR struc:

1 models

Authors:

T.Nagata,Y.Kurihara,G.Matsuda,J.Saeki,T.Kohno,Y.Yanagida,F.Ishikawa, S.Uesugi,M.Katahira

Key ref:

T.Nagata et al. (1999). Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0. J Mol Biol, 287, 221-237. PubMed id: 10080887 DOI: 10.1006/jmbi.1999.2616

Date:

18-May-99 Release date: 18-May-00

Protein chain

Q14103  (HNRPD_HUMAN) -  Heterogeneous nuclear ribonucleoprotein D0 from Homo sapiens

Seq: 355 a.a.

Struc: 75 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1999.2616

J Mol Biol 287:221-237 (1999)

PubMed id: 10080887

Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0.

T.Nagata, Y.Kurihara, G.Matsuda, J.Saeki, T.Kohno, Y.Yanagida, F.Ishikawa, S.Uesugi, M.Katahira.

ABSTRACT

Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), each of which can bind solely to the UUAG sequence specifically. The structure of the N-terminal RBD (RBD1) determined by NMR is presented here. It folds into a compact alphabeta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of the RNP-type RBDs. Special structural features of RBD1 include N-capping boxes for both alpha-helices, a beta-bulge in the second beta-strand, and an additional short antiparallel beta-sheet coupled with a beta-turn-like structure in a loop. Two hydrogen bonds which restrict the positions of loops were identified. Backbone resonance assignments for RBD1 complexed with r(UUAGGG) revealed that the overall folding is maintained in the complex. The candidate residues involved in the interactions with RNA were identified by chemical shift perturbation analysis. They are located in the central and peripheral regions of the RNA-binding surface composed of the four-stranded beta-sheet, loops, and the C-terminal region. It is suggested that non-specific interactions with RNA are performed by the residues in the central region of the RNA-binding surface, while specific interactions are performed by those in the peripheral regions. It was also found that RBD1 has the ability to inhibit the formation of the quadruplex structure.

Selected figure(s)

Figure 2.
Figure 2. The four-stranded antiparallel β-sheet of p112. Interstrand NOEs are indicated by double-headed arrows. Slowly exchanging amide protons are indicated by bold Hs. Hydrogen bonds consistent with the NOEs and exchange data are indicated by broken lines. Circles for C^α indicate that the side-chains of these residues are presumed to be exposed to the solvent.

Figure 3.
Figure 3. The structure of the 29–103 region of p112. (a) Superposition of the main-chains of 20 refined structures for the residues 29–103. N and C indicate K29 and A103, respectively, and loop 3 is labeled. (b) Schematic drawing of the restrained energy minimized mean structure derived from the 20 refined structures for 29–103, as viewed from the same direction as 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. The α-helices and β-strands are colored in red and blue, respectively. (d) Hydrophobic patch exposed to the solvent. The same overlaying as in (c) is shown for F31, F71 and F73, being rotated by ca. 90 ° from (c).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 287, 221-237) copyright 1999.

Figures were selected by an automated process.