ジャーナル: Nat Commun / 年: 2017 タイトル: Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. 著者: Zhaoyang Sun / Kamel El Omari / Xiaoyu Sun / Serban L Ilca / Abhay Kotecha / David I Stuart / Minna M Poranen / Juha T Huiskonen / 要旨: Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by ...Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.
#200 - 2016年8月 正二十面体型ウイルスの準対称性 (Quasisymmetry in Icosahedral Viruses) 類似性 (2)
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集合体
登録構造単位
A: Major inner protein P1 B: Major inner protein P1 C: Packaging enzyme P4 D: Major outer capsid protein E: Major outer capsid protein F: Major outer capsid protein G: Major outer capsid protein H: Major outer capsid protein I: Major outer capsid protein J: Major outer capsid protein K: Major outer capsid protein L: Major outer capsid protein M: Major outer capsid protein
A: Major inner protein P1 B: Major inner protein P1 C: Packaging enzyme P4 D: Major outer capsid protein E: Major outer capsid protein F: Major outer capsid protein G: Major outer capsid protein H: Major outer capsid protein I: Major outer capsid protein J: Major outer capsid protein K: Major outer capsid protein L: Major outer capsid protein M: Major outer capsid protein
A: Major inner protein P1 B: Major inner protein P1 C: Packaging enzyme P4 D: Major outer capsid protein E: Major outer capsid protein F: Major outer capsid protein G: Major outer capsid protein H: Major outer capsid protein I: Major outer capsid protein J: Major outer capsid protein K: Major outer capsid protein L: Major outer capsid protein M: Major outer capsid protein
x 5
icosahedral pentamer
1.83 MDa, 65 ポリマー
分子量 (理論値)
分子数
合計 (水以外)
1,827,720
65
ポリマ-
1,827,720
65
非ポリマー
0
0
水
0
タイプ
名称
対称操作
数
identity operation
1_555
x,y,z
1
point symmetry operation
4
4
A: Major inner protein P1 B: Major inner protein P1 C: Packaging enzyme P4 D: Major outer capsid protein E: Major outer capsid protein F: Major outer capsid protein G: Major outer capsid protein H: Major outer capsid protein I: Major outer capsid protein J: Major outer capsid protein K: Major outer capsid protein L: Major outer capsid protein M: Major outer capsid protein
∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name H-M: P1
CTF補正
タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択
選択した粒子像数: 16466
対称性
点対称性: I (正20面体型対称)
3次元再構成
解像度: 4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 13291 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT
原子モデル構築
ID
プロトコル
空間
詳細
1
RIGIDBODYFIT
REAL
The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
2
ABINITIOMODEL
REAL
The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
3
ABINITIOMODEL
The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.