4BCU

Satellite Tobacco Necrosis Virus (STNV) virus like particle in complex with the B3 aptamer

PDB DOI: 10.2210/pdb4BCU/pdb

Classification: VIRUS
Organism(s): Satellite tobacco mosaic virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-10-03 Released: 2013-01-23
Deposition Author(s): Ford, R.J., Barker, A.M., Bakker, S.E., Coutts, R.H., Ranson, N.A., Phillips, S.E.V., Pearson, A.R., Stockley, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.198
R-Value Work: 0.155
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Sequence-Specific, RNA-Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein.

Ford, R.J., Barker, A.M., Bakker, S.E., Coutts, R.H., Ranson, N.A., Phillips, S.E.V., Pearson, A.R., Stockley, P.G.

(2013) J Mol Biol 425: 1050

PubMed: 23318955 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.jmb.2013.01.004
Primary Citation of Related Structures:
4BCU

PubMed Abstract:

We have examined the roles of RNA-coat protein (CP) interactions in the assembly of satellite tobacco necrosis virus (STNV). The viral genomic RNA encodes only the CP, which comprises a β-barrel domain connected to a positively charged N-terminal extension. In the previous crystal structures of this system, the first 11 residues of the protein are disordered. Using variants of an RNA aptamer sequence isolated against the CP, B3, we have studied the sequence specificity of RNA-induced assembly. B3 consists of a stem-loop presenting the tetra-loop sequence ACAA. There is a clear preference for RNAs encompassing this loop sequence, as measured by the yield of T=1 capsids, which is indifferent to sequences within the stem. The B3-containing virus-like particle has been crystallised and its structure was determined to 2.3Å. A lower-resolution map encompassing density for the RNA has also been calculated. The presence of B3 results in increased ordering of the N-terminal helices located at the particle 3-fold axes, which extend by roughly one and a half turns to encompass residues 8-11, including R8 and K9. Under assembly conditions, STNV CP in the absence of RNA is monomeric and does not self-assemble. These facts suggest that a plausible model for assembly initiation is the specific RNA-induced stabilisation of a trimeric capsomere. The basic nature of the helical extension suggests that electrostatic repulsion between CPs prevents assembly in the absence of RNA and that this barrier is overcome by correct placement of appropriately orientated helical RNA stems. Such a mechanism would be consistent with the data shown here for assembly with longer RNA fragments, including an STNV genome. The results are discussed in light of a first stage of assembly involving compaction of the genomic RNA driven by multiple RNA packaging signal-CP interactions.

Organizational Affiliation:

Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COAT PROTEIN	A	196	Satellite tobacco mosaic virus	Mutation(s): 0
UniProt
Find proteins for P03606 (Satellite tobacco necrosis virus 1) Explore P03606 Go to UniProtKB: P03606
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03606
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction