PDBsum entry 1fj7

Structural protein

PDB id: 1fj7

Contents

Protein chain

101 a.a. *

* Residue conservation analysis

PDB id:

1fj7

Name:

Structural protein

Title:

Solution structure of nucleolin rbd1

Structure:

Nucleolin rbd1. Chain: a. Synonym: protein c23. Engineered: yes

Source:

Mesocricetus auratus. Golden hamster. Organism_taxid: 10036. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

34 models

Authors:

F.H.-T.Allain,D.E.Gilbert,P.Bouvet,J.Feigon

Key ref:

F.H.Allain et al. (2000). Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target. J Mol Biol, 303, 227-241. PubMed id: 11023788 DOI: 10.1006/jmbi.2000.4118

Date:

07-Aug-00 Release date: 16-Oct-00

Protein chain

P08199  (NUCL_MESAU) -  Nucleolin from Mesocricetus auratus

Seq: 714 a.a.

Struc: 101 a.a.*

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.2000.4118

J Mol Biol 303:227-241 (2000)

PubMed id: 11023788

Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target.

F.H.Allain, D.E.Gilbert, P.Bouvet, J.Feigon.

ABSTRACT

Nucleolin is an abundant 70 kDa nucleolar protein involved in many aspects of ribosomal RNA biogenesis. The central region of nucleolin contains four tandem consensus RNA-binding domains (RBD). The two most N-terminal domains (RBD12) bind with nanomolar affinity to an RNA stem-loop containing the consensus sequence UCCCGA in the loop. We have determined the solution structure of nucleolin RBD12 in its free form and have studied its interaction with a 22 nt RNA stem-loop using multidimensional NMR spectroscopy. The two RBDs adopt the expected beta alpha beta beta alpha beta fold, but the position of the beta 2 strand in both domains differs from what was predicted from sequence alignments. RBD1 and RBD2 are significantly different from each others and this is likely important in their sequence specific recognition of the RNA. RBD1 has a longer alpha-helix 1 and a shorter beta 2-beta 3 loop than RBD2, and differs from most other RBDs in these respects. The two RBDs are separated by a 12 amino acid flexible linker and do not interact with one another in the free protein. This linker becomes ordered when RBD12 binds to the RNA. Analysis of the observed NOEs between the protein and the RNA indicates that both RBDs interact with the RNA loop via their beta-sheet. Each domain binds residues on one side of the loop; specifically, RBD2 contacts the 5' side and RBD1 contacts the 3'.

Selected figure(s)

Figure 1.
Figure 1. (a) Schematic diagram of the domain structure of nucleolin. (b) Consensus RNA secondary structure and loop sequence found for nucleolin binding, the nucleolin recognition element (NRE) [Ghisolfi-Nieto et al 1996]. (c) Amino acid sequence of the protein constructs of RBD1, RBD2 and RBD12 from hamster nucleolin. The numbering in each RBD corresponds to the position in the RBD12 protein. Amino acid residues of RBD1, RBD2 and the linker are colored in black, red and green, respectively. Secondary structure elements are indicated below the sequence.

Figure 3.
Figure 3. Stereoviews of the family of lowest energy structures of (a) RBD1 and (b) RBD2. The 34 lowest energy structures of RBD1 are shown superimposed on the backbone heavy atoms of residue 14 to 87. The 33 lowest energy structures of RBD2 are superimposed on the backbone heavy atoms of residue 93 to 171. The location of a-helix 1 (cyan), a-helix 2 (red) and the first and last residues are indicated. The b2-b3 loop is colored orange and the N-terminal helix on RBD2 is green. (c) Ribbon representation of RBD12. Since the linker region (green) is flexible and no NOEs are observed between the two RBDs, the orientation of the two RBDs relative to one another is not defined in solution. The structure shown has the two RBDs oriented in such a way that their b-strands can interact with the RNA. Side-chains of F17, Y58, L103, and Y140 shown on the structure have intermolecular NOEs to the RNA loop nucleotides (Figure 7).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 227-241) copyright 2000.

Figures were selected by an automated process.