2K47

Solution structure of the C-terminal N-RNA binding domain of the Vesicular Stomatitis Virus Phosphoprotein

DOI: 10.2210/pdb2K47/pdb

Classification: REPLICATION
Organism(s): Vesicular stomatitis Indiana virus strain San Juan
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-28 Released: 2008-09-09
Deposition Author(s): Ribeiro, E.A., Favier, A., Gerard, F.C., Leyrat, C., Brutscher, B., Blondel, D., Ruigrok, R.W., Blackledge, M., Jamin, M.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 500
Conformers Submitted: 20
Selection Criteria: 20 structures for lowest energy

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Solution Structure of the C-Terminal Nucleoprotein-RNA Binding Domain of the Vesicular Stomatitis Virus Phosphoprotein.

Ribeiro, E.A., Favier, A., Gerard, F.C., Leyrat, C., Brutscher, B., Blondel, D., Ruigrok, R.W., Blackledge, M., Jamin, M.

(2008) J Mol Biol

PubMed: 18657547 Search on PubMed
DOI: 10.1016/j.jmb.2008.07.028
Primary Citation of Related Structures:
2K47

PubMed Abstract:

Beyond common features in their genome organization and replication mechanisms, the evolutionary relationships among viruses of the Rhabdoviridae family are difficult to decipher because of the great variability in the amino acid sequence of their proteins. The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential component of the RNA transcription and replication machinery; in particular, it contains binding sites for the RNA-dependent RNA polymerase and for the nucleoprotein. Here, we devised a new method for defining boundaries of structured domains from multiple disorder prediction algorithms, and we identified an autonomous folding C-terminal domain in VSV P (P(CTD)). We show that, like the C-terminal domain of rabies virus (RV) P, VSV P(CTD) binds to the viral nucleocapsid (nucleoprotein-RNA complex). We solved the three-dimensional structure of VSV P(CTD) by NMR spectroscopy and found that the topology of its polypeptide chain resembles that of RV P(CTD). The common part of both proteins could be superimposed with a backbone RMSD from mean atomic coordinates of 2.6 A. VSV P(CTD) has a shorter N-terminal helix (alpha(1)) than RV P(CTD); it lacks two alpha-helices (helices alpha(3) and alpha(6) of RV P), and the loop between strands beta(1) and beta(2) is longer than that in RV. Dynamical properties measured by NMR relaxation revealed the presence of fast motions (below the nanosecond timescale) in loop regions (amino acids 209-214) and slower conformational exchange in the N- and C-terminal helices. Characterization of a longer construct indicated that P(CTD) is preceded by a flexible linker. The results presented here support a modular organization of VSV P, with independent folded domains separated by flexible linkers, which is conserved among different genera of Rhabdoviridae and is similar to that proposed for the P proteins of the Paramyxoviridae.

Organizational Affiliation:

UJF-EMBL-CNRS-UMR 5233-Unit of Virus Host Cell Interactions, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoprotein	A	79	Vesicular stomatitis Indiana virus strain San Juan	Mutation(s): 0 Gene Names: P
Find proteins for P03520 (Vesicular stomatitis Indiana virus (strain San Juan)) Explore P03520 Go to UniProtKB: P03520
Protein Feature View Expand
Reference Sequence