PDBsum entry 1fje

Structural protein/RNA

PDB id: 1fje

Contents

Protein chain

175 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1fje

Name:

Structural protein/RNA

Title:

Solution structure of nucleolin rbd12 in complex with snre RNA

Structure:

Snre RNA. Chain: a. Engineered: yes. Other_details: in vitro selected RNA. Nucleolin rbd12. Chain: b. Fragment: two n-terminal rbd domains. Synonym: protein c23. Engineered: yes

Source:

Synthetic: yes. Other_details: in vitro transcription by t7 RNA polymerase. Mesocricetus auratus. Golden hamster. Organism_taxid: 10036. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

19 models

Authors:

F.H.T.Allain,P.Bouvet,T.Dieckmann,J.Feigon

Key ref:

F.H.Allain et al. (2000). Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin. EMBO J, 19, 6870-6881. PubMed id: 11118222 DOI: 10.1093/emboj/19.24.6870

Date:

08-Aug-00 Release date: 03-Jan-01

Protein chain

P08199  (NUCL_MESAU) -  Nucleolin from Mesocricetus auratus

Seq: 714 a.a.

Struc: 175 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chain

G-G-C-C-G-A-A-A-U-C-C-C-G-A-A-G-U-A-G-G-C-C 22 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/19.24.6870

EMBO J 19:6870-6881 (2000)

PubMed id: 11118222

Molecular basis of sequence-specific recognition of pre-ribosomal RNA by nucleolin.

F.H.Allain, P.Bouvet, T.Dieckmann, J.Feigon.

ABSTRACT

The structure of the 28 kDa complex of the first two RNA binding domains (RBDs) of nucleolin (RBD12) with an RNA stem-loop that includes the nucleolin recognition element UCCCGA in the loop was determined by NMR spectroscopy. The structure of nucleolin RBD12 with the nucleolin recognition element (NRE) reveals that the two RBDs bind on opposite sides of the RNA loop, forming a molecular clamp that brings the 5' and 3' ends of the recognition sequence close together and stabilizing the stem-loop. The specific interactions observed in the structure explain the sequence specificity for the NRE sequence. Binding studies of mutant proteins and analysis of conserved residues support the proposed interactions. The mode of interaction of the protein with the RNA and the location of the putative NRE sites suggest that nucleolin may function as an RNA chaperone to prevent improper folding of the nascent pre-rRNA.

Selected figure(s)

Figure 3.
Figure 3 Overall description of the complex. The lowest energy structure is shown. (A) Stick (RNA) and ribbon (protein) representation of the complex showing how the RNA loop is 'sandwiched' between the two RBDs. RBD1 is located in the major groove side of the RNA and contacts C12, G13 and the loop E motif. RBD2 is located on the minor groove side and contacts U9 and C10. The linker is mostly located in the minor groove side on the RNA. The amino acid side chains from RBD1 V27, K31 ( -helix 1) and T52, R54 ( 2– 3 loop), which contact the stem, as well as the inserting residues F56 and K94, are shown in blue. (B) Surface representation of the RNA and protein complex. The view is the same as in (A). (C) View of the complex showing that the two RBDs interact via two salt bridges (K89–E125 and K55–D132). Asp and Glu are shown in red and Lys and Arg in blue. The major groove face of the binding site is shown. (D) GRASP (Nicholls et al., 1991) representation of the complex with positively charged residues in blue and negatively charged residues in red. The color scheme is the same as Figure 2, except for the GRASP representation.

Figure 8.
Figure 8 Proposed model of the RNA chaperone activity of nucleolin for proper folding of the 5' ETS region between nucleotides 1671 and 3549 of human 47S pre-rRNA. A schematic representation of the predicted secondary structure of this region in the mature pre-rRNA based on phylogeny (Renalier et al., 1989) and electron microscopy (Wellauer et al., 1974; Schibler et al., 1975) studies is shown on the right. The putative NRE binding sites in this sequence are indicated by black rectangles. They are all found in double-stranded regions of the mature pre-rRNA, so nucleolin (indicated by the black oval ring) is not expected to be bound. On the left side of the figure are shown schematically two alternate structures that the RNA can adopt with (top) or without (bottom) nucleolin. Without nucleolin, the RNA can be kinetically trapped in alternative stable structures, which have to unfold to form the mature pre-rRNA, with the result that formation of the mature pre-rRNA will be slow. The bound nucleolin promotes and/or stabilizes stem–loops at the NRE consensus sites, preventing the formation of alternative stable helices, and then dissociates to allow the final structure to form.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 6870-6881) copyright 2000.

Figures were selected by an automated process.