PDBsum entry 1wvn

RNA binding protein

PDB id: 1wvn

Contents

Protein chain

74 a.a. *

Waters ×55

* Residue conservation analysis

PDB id:

1wvn

Name:

RNA binding protein

Title:

Crystal structure of domain 3 of human alpha polyc binding protein

Structure:

Poly(rc)-binding protein 1. Chain: a. Fragment: domain 3 (residues 279-356). Synonym: alpha-cp1, hnrnp-e1, nucleic acid binding protein sub2.3. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.214 R-free: 0.248

Authors:

M.C.J.Wilce,J.A.Wilce,M.Sidiqu

Key ref:

M.Sidiqi et al. (2005). Structure and RNA binding of the third KH domain of poly(C)-binding protein 1. Nucleic Acids Res, 33, 1213-1221. PubMed id: 15731341

Date:

17-Dec-04 Release date: 05-Apr-05

Protein chain

Q15365  (PCBP1_HUMAN) -  Poly(rC)-binding protein 1 from Homo sapiens

Seq: 356 a.a.

Struc: 74 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

Nucleic Acids Res 33:1213-1221 (2005)

PubMed id: 15731341

Structure and RNA binding of the third KH domain of poly(C)-binding protein 1.

M.Sidiqi, J.A.Wilce, J.P.Vivian, C.J.Porter, A.Barker, P.J.Leedman, M.C.Wilce.

ABSTRACT

Poly(C)-binding proteins (CPs) are important regulators of mRNA stability and translational regulation. They recognize C-rich RNA through their triple KH (hn RNP K homology) domain structures and are thought to carry out their function though direct protection of mRNA sites as well as through interactions with other RNA-binding proteins. We report the crystallographically derived structure of the third domain of alphaCP1 to 2.1 A resolution. alphaCP1-KH3 assumes a classical type I KH domain fold with a triple-stranded beta-sheet held against a three-helix cluster in a betaalphaalphabetabetaalpha configuration. Its binding affinity to an RNA sequence from the 3'-untranslated region (3'-UTR) of androgen receptor mRNA was determined using surface plasmon resonance, giving a K(d) of 4.37 microM, which is indicative of intermediate binding. A model of alphaCP1-KH3 with poly(C)-RNA was generated by homology to a recently reported RNA-bound KH domain structure and suggests the molecular basis for oligonucleotide binding and poly(C)-RNA specificity.

Selected figure(s)

Figure 1.
The crystal structure of Å resolution depicted in (A) cartoon form and (B) as a molecular surface in the same orientation. The structure is shown from the beginning of ß-strand 1 to the end of {alpha} -helix 3, since the regions outside these bounds were random coil or not visible in the density. The GXXG motif, common to this oligonucleotide-binding motif, is coloured blue. The `variable loop' region between ß-sheets 2 and 3 is coloured pink. These regions bound the hydrophobic oligonucleotide-binding cleft that accommodates C-rich RNA or ssDNA. (C) The electrostatic potential emanating from the {alpha} CP1-KH3 structure calculated using the APBS software package (http://agave.wustl.edu/apbs/) (39-43). Potential contours are shown at +1 kT/e (blue) and -1 kT/e (red) and obtained by solution of the linearized Poisson-Boltzmann equation at 150 mM ionic strength with a solute dielectric of 2 and a solvent dielectric of 78.5. The blue contour represents a striking positive potential directing oligonucleotides to the binding cleft.

Figure 4.
Interaction of the measured by surface plasmon resonance. (A) 30 RU RNA was immobilized on a streptavidin-coated chip. Binding interactions were measured for a series of dilutions of the {alpha} CP1-KH3 domain from 10 to 0.625 µM for 2 min using flow rate of 50 µl/min. (B) Steady-state analysis of the interaction yielded a K[d] value of 4.37 µM.

The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 1213-1221) copyright 2005.

Figures were selected by an automated process.