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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-0174 | |||||||||||||||
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タイトル | Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution. | |||||||||||||||
![]() | Centered map 0 0 0 | |||||||||||||||
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![]() | vertical single beta-barrel virus / internal membrane-containing archaeal virus. / VIRUS | |||||||||||||||
機能・相同性 | VP7 / VP4 / VP9![]() | |||||||||||||||
生物種 | ![]() ![]() | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.74 Å | |||||||||||||||
![]() | Abrescia NG / Santos-Perez I / Charro D / Azkargorta M / Elortza F / Bamford DH / Oksanen HM / Abrescia NGA | |||||||||||||||
資金援助 | ![]() ![]()
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![]() | ![]() タイトル: Structural basis for assembly of vertical single β-barrel viruses. 著者: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia / ![]() ![]() 要旨: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. | |||||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 1.6 GB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 29.1 KB 29.1 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 27 KB | 表示 | ![]() |
画像 | ![]() | 197.5 KB | ||
マスクデータ | ![]() | 1.7 GB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
その他 | ![]() ![]() ![]() | 1.6 GB 1.4 GB 1.4 GB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 34.7 KB | 表示 | |
CIF形式データ | ![]() | 47.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Centered map 0 0 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #1
ファイル | emd_0174_additional.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: None
ファイル | emd_0174_half_map_1.map | ||||||||||||
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注釈 | None | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: None
ファイル | emd_0174_half_map_2.map | ||||||||||||
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注釈 | None | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : Haloarcula californiae icosahedral virus 1
全体 | 名称: ![]() |
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要素 |
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-超分子 #1: Haloarcula californiae icosahedral virus 1
超分子 | 名称: Haloarcula californiae icosahedral virus 1 / タイプ: virus / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: Haloarcula californiae icosahedral virus - 1 / NCBI-ID: 662475 / 生物種: Haloarcula californiae icosahedral virus 1 / ウイルスタイプ: VIRION / ウイルス・単離状態: SPECIES / ウイルス・エンベロープ: No / ウイルス・中空状態: No |
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宿主 | 生物種: ![]() |
ウイルス殻 | Shell ID: 1 / 直径: 800.0 Å / T番号(三角分割数): 28 |
-分子 #1: VP7
分子 | 名称: VP7 / タイプ: protein_or_peptide / ID: 1 / コピー数: 15 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 19.912832 KDa |
配列 | 文字列: MGNIGNLSAE KQISLYDGQP FISEQDVAAG DPNTPALTIE GPDGYVIAVD AGTPIAPEFR DSNGEKLDPS TRVIVQKCDR QGNPLGDGI IFNDTLGRFN YNKMRTDPDY MRKTAKSLMV DEREIVKVFV DVPDGANGYD AERSRFTLGD DTSDFGKAVE I VDHDDLTE GETQAVKSAS QRSGGA UniProtKB: VP7 |
-分子 #2: VP9
分子 | 名称: VP9 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 16.271062 KDa |
配列 | 文字列: MRDNQDLLVK RLGRLVNVLE SKEFGGTTTV DKDLDVTKNV TRTDEPNEDN TPDYFSTGKD RVLVPDTEEW ERLGFGIVAK TVNVRTTDD VLLAFANPNT NGPTFKIRSN ESPFTIGGDA GIDTAFMWLK KAESAQNDPA VEIIAYR UniProtKB: VP9 |
-分子 #3: GPS-III molecule located underneath the capsomer close to the ico...
分子 | 名称: GPS-III molecule located underneath the capsomer close to the icosahedral three-fold axis. タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 9.209344 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) |
-分子 #4: GPS-II protein located underneath the two-tower capsomer NOT sitt...
分子 | 名称: GPS-II protein located underneath the two-tower capsomer NOT sitting on the icosahedral 2-fold axis. タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 6.400881 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-分子 #5: (Half) GPS-II protein located underneath the two-tower capsomer s...
分子 | 名称: (Half) GPS-II protein located underneath the two-tower capsomer sitting ON the icosahedral 2-fold axis. タイプ: protein_or_peptide / ID: 5 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 3.932839 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-分子 #6: Peripentonal unknown polypeptide
分子 | 名称: Peripentonal unknown polypeptide / タイプ: protein_or_peptide / ID: 6 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 1.549902 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) |
-分子 #7: VP4
分子 | 名称: VP4 / タイプ: protein_or_peptide / ID: 7 / コピー数: 12 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 25.995318 KDa |
配列 | 文字列: MADQTQEYTL SHTGGLLGSS KVTTASNQTA PQRETAIISF EVPRKFSEIE YVGQRDATRF VPRTTEEITG TANDDTVVQL QANIQPIAG EEDMADQDYP VVVAYNVTQG AQVEIADVNY ATDEVTLATD PADGDTVKLW PIMGDGEVQF RLVNQFGQEE G RVYPWATP ...文字列: MADQTQEYTL SHTGGLLGSS KVTTASNQTA PQRETAIISF EVPRKFSEIE YVGQRDATRF VPRTTEEITG TANDDTVVQL QANIQPIAG EEDMADQDYP VVVAYNVTQG AQVEIADVNY ATDEVTLATD PADGDTVKLW PIMGDGEVQF RLVNQFGQEE G RVYPWATP LYRWHDFPQL KRGREINLHG SVTWQENETV EVLLDAPQAI TWEDADYPEG QYVSTFEQDV EITL UniProtKB: VP4 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 1.2 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 7.2 構成要素:
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凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK III | ||||||||||||||||||
詳細 | Haloarcula californiae icosahedral virus 1. Taxonomic identifier 1735722 NCBI. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - 画像ごとのフレーム数: 1-26 / 撮影したグリッド数: 1 / 実像数: 3218 / 平均電子線量: 36.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.9 µm / 最小 デフォーカス(公称値): 0.6 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
詳細 | The HCIV-1 VP7 and VP4 MCPs were manually built aided by beta-barrel core templates derived from the crystal structures of Thermus bacteriophage P23-77 MCPs (PDB ID 3ZN6). |
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精密化 | 空間: REAL / プロトコル: AB INITIO MODEL / 温度因子: 89.1 当てはまり具合の基準: Cross-correlation coefficient |
得られたモデル | ![]() PDB-6h9c: |