PDBsum entry 3fbz

Structural protein

PDB id: 3fbz

Contents

Protein chains

123 a.a.

Ligands

BOG ×8

Metals

_CL ×2

Waters ×243

PDB id:

3fbz

Name:

Structural protein

Title:

Crystal structure of orf140 of the archaeal virus acidianus filamentous virus 1 (afv1)

Structure:

Putative uncharacterized protein. Chain: a, b, c, d. Synonym: orf140. Engineered: yes

Source:

Acidianus filamentous virus 1. Organism_taxid: 235266. Gene: afv1_orf140. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.188 R-free: 0.255

Authors:

A.Goulet,D.Prangishvili,H.Van Tilbeurgh,V.Campanacci,C.Cambillau

Key ref:

A.Goulet et al. (2009). Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc Natl Acad Sci U S A, 106, 21155-21160. PubMed id: 19934032 DOI: 10.1073/pnas.0909893106

Date:

20-Nov-08 Release date: 10-Nov-09

Protein chains

Q70LC6  (CAPS1_AFV1Y) -  Major capsid protein 1 from Acidianus filamentous virus 1 (isolate United States/Yellowstone)

Seq: 140 a.a.

Struc: 123 a.a.

DOI no: 10.1073/pnas.0909893106

Proc Natl Acad Sci U S A 106:21155-21160 (2009)

PubMed id: 19934032

Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.

A.Goulet, S.Blangy, P.Redder, D.Prangishvili, C.Felisberto-Rodrigues, P.Forterre, V.Campanacci, C.Cambillau.

ABSTRACT

Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.

Selected figure(s)

Figure 2.
Crystal structure of ΔN_AFV1–132. (A) Ribbon representation of ΔN_AFV1–132 crystal structure with a rainbow color gradient from the N terminus (blue) to the C terminus (red). Helices are sequentially labeled α1 to α4. Tyr-51 is the first residue seen in the electron density map. (B) ΔN_AFV1–132 crystal structure (cyan) superimposed onto ΔN_SIRV-134 (residues 52–134) crystal structure (light green) with a r.m.s deviation of 1.4 Å on the Cα backbone. (C and D) Electrostatic surfaces of ΔN_AFV1–132 and ΔN_SIRV-134, respectively, in the same orientation. Figs. were created with Pymol, http://pymol.sourceforge.net/.

Figure 3.
Crystal structure of AFV1–140. (A) AFV1–140 crystal structure (gray) superimposed onto ΔN_AFV1–132 (cyan) with a r.m.s deviation of 1.54 Å on the Cα backbone. Helices are sequentially labeled α'1 to α'5. (B) Electrostatic surface in the same orientation. (C) Head-to-tail dimer in which one chain is shown as a gray ribbon and the other is represented as light green surface. (D) Tetramer of the asymmetric unit is composed of a dimer of dimers. Detergent molecules (β-OG) are represented with orange surfaces. Figs. were created with Pymol.

Figures were selected by an automated process.