ジャーナル: Nat Commun / 年: 2023 タイトル: Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style. 著者: Sara Pfister / Julius Rabl / Thomas Wiegand / Simone Mattei / Alexander A Malär / Lauriane Lecoq / Stefan Seitz / Ralf Bartenschlager / Anja Böckmann / Michael Nassal / Daniel Boehringer / Beat H Meier / 要旨: The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV ...The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV acquired an envelope during evolution, nackednaviruses remained non-enveloped. We report the capsid structure of the African cichlid nackednavirus (ACNDV), determined by cryo-EM at 3.7 Å resolution. This enables direct comparison with the known capsid structures of HBV and duck HBV, prototypic representatives of the mammalian and avian lineages of the enveloped Hepadnaviridae, respectively. The sequence identity with HBV is 24% and both the ACNDV capsid protein fold and the capsid architecture are very similar to those of the Hepadnaviridae and HBV in particular. Acquisition of the hepadnaviral envelope was thus not accompanied by a major change in capsid structure. Dynamic residues at the spike tip are tentatively assigned by solid-state NMR, while the C-terminal domain is invisible due to dynamics. Solid-state NMR characterization of the capsid structure reveals few conformational differences between the quasi-equivalent subunits of the ACNDV capsid and an overall higher capsid structural disorder compared to HBV. Despite these differences, the capsids of ACNDV and HBV are structurally highly similar despite the 400 million years since their separation.
1A: C protein AC: C protein BA: C protein BB: C protein BC: C protein CA: C protein CB: C protein CC: C protein DA: C protein DB: C protein DC: C protein EA: C protein EB: C protein EC: C protein FA: C protein FB: C protein FC: C protein GA: C protein GB: C protein GC: C protein HA: C protein HB: C protein HC: C protein IA: C protein IB: C protein IC: C protein JA: C protein 1B: C protein JB: C protein JC: C protein KA: C protein KB: C protein KC: C protein LA: C protein LB: C protein LC: C protein MA: C protein MB: C protein MC: C protein NA: C protein NB: C protein NC: C protein OA: C protein OB: C protein OC: C protein PA: C protein PB: C protein PC: C protein QA: C protein QB: C protein QC: C protein RA: C protein RB: C protein RC: C protein 1C: C protein SA: C protein SB: C protein SC: C protein TA: C protein TB: C protein TC: C protein UA: C protein UB: C protein UC: C protein VA: C protein VB: C protein VC: C protein WA: C protein WB: C protein WC: C protein XA: C protein XB: C protein XC: C protein YA: C protein YB: C protein YC: C protein ZA: C protein ZB: C protein ZC: C protein aA: C protein aB: C protein 2A: C protein aC: C protein bA: C protein bB: C protein bC: C protein cA: C protein cB: C protein cC: C protein dA: C protein dB: C protein dC: C protein eA: C protein eB: C protein eC: C protein fA: C protein fB: C protein fC: C protein gA: C protein gB: C protein gC: C protein hA: C protein hB: C protein hC: C protein iA: C protein iB: C protein iC: C protein jA: C protein 2B: C protein jB: C protein jC: C protein kA: C protein kB: C protein kC: C protein lA: C protein lB: C protein lC: C protein mA: C protein mB: C protein mC: C protein nA: C protein nB: C protein nC: C protein oA: C protein oB: C protein oC: C protein pA: C protein pB: C protein pC: C protein qA: C protein qB: C protein qC: C protein rA: C protein rB: C protein rC: C protein 2C: C protein sA: C protein sB: C protein sC: C protein tA: C protein tB: C protein tC: C protein uA: C protein uB: C protein uC: C protein vA: C protein vB: C protein vC: C protein wA: C protein wB: C protein wC: C protein xA: C protein xB: C protein xC: C protein yA: C protein yB: C protein yC: C protein zA: C protein zB: C protein zC: C protein 3A: C protein 3B: C protein 3C: C protein 4A: C protein 4B: C protein 4C: C protein 5A: C protein 5B: C protein 5C: C protein 6A: C protein 6B: C protein 6C: C protein 7A: C protein 7B: C protein 7C: C protein 8A: C protein 8B: C protein 8C: C protein AA: C protein AB: C protein
電子線照射量: 55 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 実像数: 5362
電子光学装置
エネルギーフィルタースリット幅: 20 eV
画像スキャン
動画フレーム数/画像: 40 / 利用したフレーム数/画像: 1-40
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解析
EMソフトウェア
ID
名称
バージョン
カテゴリ
1
crYOLO
1.7.6
粒子像選択
2
EPU
画像取得
4
Gctf
1.06
CTF補正
7
Coot
0.8.9
モデルフィッティング
9
PHENIX
1.17.1-3660
モデル精密化
10
ISOLDE
1.0b4.dev0
モデル精密化
11
RELION
3.1
初期オイラー角割当
12
RELION
3.1
最終オイラー角割当
13
RELION
3.1
分類
14
RELION
3.1
３次元再構成
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: 215225
対称性
点対称性: I (正20面体型対称)
3次元再構成
解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 77129 / クラス平均像の数: 1 / 対称性のタイプ: POINT
原子モデル構築
プロトコル: AB INITIO MODEL / 空間: REAL 詳細: One protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid was refined with phenix and Isolde.
ムービー
コントローラー
データを開く
基本情報
要素
キーワード
機能・相同性情報
African cichlid nackednavirus (ウイルス)
データ登録者
スイス, 3件 
引用
構造の表示
ダウンロードとリンク
その他のダウンロード
PDBj
集合体
Escherichia coli (大腸菌) / 参照: UniProt: A0A3S9H6T3
試料調製
電子顕微鏡撮影
FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
解析