4Y5Z image
Deposition Date 2015-02-12
Release Date 2016-01-20
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4Y5Z
Keywords:
VIRUS
Title:
T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the N-terminus (P1 crystal form)
Biological Source:
Source Organism:
Staphylococcus aureus (Taxon ID: 93061)
Sesbania mosaic virus (Taxon ID: 12558)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.95 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1
4Y5Z validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Immunoglobulin G-binding protein A,Coat protein
Gene (Uniprot):spa
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA (auth: a), BA (auth: c), CA (auth: e), DA (auth: g), EA (auth: i), FA (auth: k), GA (auth: m), HA (auth: o), IA (auth: q), JA (auth: r), KA (auth: s), LA (auth: t), MA (auth: u), NA (auth: v), OA (auth: w), PA (auth: x), QA (auth: y), RA (auth: z), SA (auth: 0), TA (auth: 1), UA (auth: 2), VA (auth: 3), WA (auth: 4), XA (auth: 5), YA (auth: 6), ZA (auth: 7), AB (auth: b), BB (auth: d), CB (auth: f), DB (auth: h), EB (auth: j), FB (auth: l), GB (auth: n), HB (auth: p)
Chain Length:282
Number of Molecules:60
Biological Source:Staphylococcus aureus, Sesbania mosaic virus
UniProt ID:P02976,Q9EB06 Pfam ID:PF02216, PF00729
Ligand Molecules
SO4
Primary Citation
Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly.
Virology 489 34 43 (2015)
PMID: 26704627 DOI: 10.1016/j.virol.2015.11.029

Abstact

The capsid protein (CP) of Sesbania mosaic virus (SeMV, a T=3 plant virus) consists of a disordered N-terminal R-domain and an ordered S-domain. Removal of the R-domain results in the formation of T=1 particles. In the current study, the R-domain was replaced with unrelated polypeptides of similar lengths: the B-domain of Staphylococcus aureus SpA, and SeMV encoded polypeptides P8 and P10. The chimeric proteins contained T=3 or larger virus-like particles (VLPs) and could not be crystallized. The presence of metal ions during purification resulted in a large number of heterogeneous nucleoprotein complexes. N∆65-B (R domain replaced with B domain) could also be purified in a dimeric form. Its crystal structure revealed T=1 particles devoid of metal ions and the B-domain was disordered. However, the B-domain was functional in N∆65-B VLPs, suggesting possible biotechnological applications. These studies illustrate the importance of N-terminal residues, metal ions and robustness of the assembly process.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4Y4Y