+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8des | ||||||
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タイトル | Gokushovirus EC6098 | ||||||
要素 |
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キーワード | VIRUS / Capsid | ||||||
機能・相同性 | Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / structural molecule activity / Major capsid protein / Putative DNA binding protein 機能・相同性情報 | ||||||
生物種 | Escherichia phage EC6098 (ファージ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | ||||||
データ登録者 | Lee, H. / Fane, B.A. / Hafenstein, S.L. | ||||||
資金援助 | 1件
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引用 | ジャーナル: J Virol / 年: 2022 タイトル: Cryo-EM Structure of Gokushovirus ΦEC6098 Reveals a Novel Capsid Architecture for a Single-Scaffolding Protein, Microvirus Assembly System. 著者: Hyunwook Lee / Alexis J Baxter / Carol M Bator / Bentley A Fane / Susan L Hafenstein / 要旨: Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of ...Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of gokushovirus ΦEC6098 was determined, and the atomic model was built . Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the ΦX174 capsid protein, the core of the ΦEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each ΦEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In ΦX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the ΦEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the ΦX174 external scaffolding protein. There were also key differences between the ΦX174-like DNA-binding J proteins and its ΦEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the ΦX174 and α3 J proteins. There is a dramatic structural and morphogenetic divide within the . The well-studied ΦX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two ΦX174 assembly proteins, but retain an internal scaffolding protein. The ΦEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8des.cif.gz | 98.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8des.ent.gz | 74 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8des.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8des_validation.pdf.gz | 991.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8des_full_validation.pdf.gz | 992.5 KB | 表示 | |
XML形式データ | 8des_validation.xml.gz | 30.7 KB | 表示 | |
CIF形式データ | 8des_validation.cif.gz | 41.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/de/8des ftp://data.pdbj.org/pub/pdb/validation_reports/de/8des | HTTPS FTP |
-関連構造データ
関連構造データ | 27397MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 63367.758 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Escherichia phage EC6098 (ファージ) 遺伝子: vp1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A6G9L6B3 |
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#2: タンパク質・ペプチド | 分子量: 4830.820 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Escherichia phage EC6098 (ファージ) 遺伝子: vp8 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A6G9L8Z7 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Escherichia phage EC6098 / タイプ: VIRUS / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Escherichia phage EC6098 (ファージ) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: NO / 単離: STRAIN / タイプ: VIRION |
緩衝液 | pH: 7 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3300 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 50 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) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 2.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 32308 / 対称性のタイプ: POINT |