2W4Z

Caulobacter bacteriophage 5

2W4Z の概要

• エントリーDOI: 10.2210/pdb2w4z/pdb
• 関連するPDBエントリー: 2W4Y
• 分子名称: CAULOBACTER BACTERIOPHAGE 5, CALCIUM ION, ADENOSINE MONOPHOSPHATE (3 entities in total)
• 機能のキーワード: virus, assembly, calcium ion, rna
• 由来する生物種: UNCLASSIFIED LEVIVIRUS
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 41698.92

構造登録者

Plevka, P.,Kazaks, A.,Dishlers, A.,Liljas, L.,Tars, K. (登録日: 2008-12-02, 公開日: 2009-07-14, 最終更新日: 2024-05-01)

主引用文献

Plevka, P.,Kazaks, A.,Voronkova, T.,Kotelovica, S.,Dishlers, A.,Liljas, L.,Tars, K.
The Structure of Bacteriophage Phicb5 Reveals a Role of the RNA Genome and Metal Ions in Particle Stability and Assembly.
J.Mol.Biol., 391:635-, 2009

PubMed Abstract: The structure of the Leviviridae bacteriophage phiCb5 virus-like particle has been determined at 2.9 A resolution and the structure of the native bacteriophage phiCb5 at 3.6 A. The structures of the coat protein shell appear to be identical, while differences are found in the organization of the density corresponding to the RNA. The capsid is built of coat protein dimers and in shape corresponds to a truncated icosahedron with T = 3 quasi-symmetry. The capsid is stabilized by four calcium ions per icosahedral asymmetric unit. One is located at the symmetry axis relating the quasi-3-fold related subunits and is part of an elaborate network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilize the contacts within the coat protein dimer. The stability of the phiCb5 particles decreases when calcium ions are chelated with EDTA. In contrast to other leviviruses, phiCb5 particles are destabilized in solution with elevated salt concentration. The model of the phiCb5 capsid provides an explanation of the salt-induced destabilization of phiCb5, since hydrogen bonds, salt bridges and calcium ions have important roles in the intersubunit interactions. Electron density of three putative RNA nucleotides per icosahedral asymmetric unit has been observed in the phiCb5 structure. The nucleotides mediate contacts between the two subunits forming a dimer and a third subunit in another dimer. We suggest a model for phiCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The phiCb5 structure is the first example in the levivirus family that provides insight into the mechanism by which the genome-coat protein interaction may accelerate the capsid assembly and increase capsid stability.

PubMed: 19559027
DOI: 10.1016/J.JMB.2009.06.047

実験手法

X-RAY DIFFRACTION (3.6 Å)