+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0650 | ||||||||||||||||||
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タイトル | Cryo-EM structure of OTOP3 from xenopus tropicalis | ||||||||||||||||||
マップデータ | Cryo-EM structure of OTOP3 from xenopus tropicalis | ||||||||||||||||||
試料 |
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キーワード | Otopetrin / proton / channel / MEMBRANE PROTEIN | ||||||||||||||||||
機能・相同性 | Otopetrin / Otopetrin / proton channel activity / proton transmembrane transport / identical protein binding / plasma membrane / Proton channel OTOP3 機能・相同性情報 | ||||||||||||||||||
生物種 | Xenopus tropicalis (ネッタイツメガエル) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.92 Å | ||||||||||||||||||
データ登録者 | Chen QF / Bai XC | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Elife / 年: 2019 タイトル: Structural and functional characterization of an otopetrin family proton channel. 著者: Qingfeng Chen / Weizhong Zeng / Ji She / Xiao-Chen Bai / Youxing Jiang / 要旨: The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from (XtOTOP3) along with functional characterization of the channel. ...The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln-Asp/Asn-Tyr (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels. | ||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0650.map.gz | 20.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0650-v30.xml emd-0650.xml | 14.5 KB 14.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0650.png | 226.6 KB | ||
Filedesc metadata | emd-0650.cif.gz | 6.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0650 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0650 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0650_validation.pdf.gz | 541.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0650_full_validation.pdf.gz | 541.1 KB | 表示 | |
XML形式データ | emd_0650_validation.xml.gz | 5.5 KB | 表示 | |
CIF形式データ | emd_0650_validation.cif.gz | 6.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0650 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0650 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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-マップ
ファイル | ダウンロード / ファイル: emd_0650.map.gz / 形式: CCP4 / 大きさ: 22.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of OTOP3 from xenopus tropicalis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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
-試料の構成要素
-全体 : Xenopus tropicalis OTOP3
全体 | 名称: Xenopus tropicalis OTOP3 |
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要素 |
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-超分子 #1: Xenopus tropicalis OTOP3
超分子 | 名称: Xenopus tropicalis OTOP3 / タイプ: organelle_or_cellular_component / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Xenopus tropicalis (ネッタイツメガエル) |
分子量 | 理論値: 77 KDa |
-分子 #1: LOC100127796 protein,LOC100127796 protein,OTOP3,LOC100127796 prot...
分子 | 名称: LOC100127796 protein,LOC100127796 protein,OTOP3,LOC100127796 protein,LOC100127796 protein タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Xenopus tropicalis (ネッタイツメガエル) |
分子量 | 理論値: 73.352297 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MLSKEEPACR QFHSREKTWG NEHNGKTVTQ ANNKEHKVPA VRRGDIGQRE PAAHPASHIQ GTMASENTGE QATCKDQYMD LDAPGNNLE HSWLHRHCEI PTTLHQRAKK TGRLFSGLFG LNLMFLGGTV VSSVALSNKA VPERDSQSFL CILMLLSSVW A LYHLLFIR ...文字列: MLSKEEPACR QFHSREKTWG NEHNGKTVTQ ANNKEHKVPA VRRGDIGQRE PAAHPASHIQ GTMASENTGE QATCKDQYMD LDAPGNNLE HSWLHRHCEI PTTLHQRAKK TGRLFSGLFG LNLMFLGGTV VSSVALSNKA VPERDSQSFL CILMLLSSVW A LYHLLFIR NQNGAVHHDH HAGAMWLKAS LAIFGVCSII LSIFEIGHAL LLQNCEILMD IVFFSIEIVF VSVQTVLLWV SC KDCVQMH HSVTRYGIML TLATDILLWL TAVIDDSLEQ DLEILQSNST QDESNEMAQC QCPTDSMCWG LKQGYVTMFP FNI EYSLIC ATLLFIMWKN VGRRE(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)W(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)R KLDVTLLFVS AVGQLGISYF SIIATVVTTP WTML SALNF SNSLLLILQY LSQTMFIIES MRSIHEEEKE KPGHHEESHR RMSVQEMHKA PPSCLDAGHL GLSRRVVKEM AMFLM ICNI MCWILGAFGA HPLYMNGLER QLYGSGIWLA ILNIGLPLSV FYRMHSVGIL LEVYLHALEG SSLVPR UniProtKB: Proton channel OTOP3, Proton channel OTOP3 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 1.3 mg/mL |
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緩衝液 | pH: 8 / 構成要素 - 濃度: 150.0 mM / 構成要素 - 式: NaCl / 構成要素 - 名称: sodium chloride 詳細: Solutions were made fresh from stock solutions and filtered. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
詳細 | This sample was monodisperse |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 撮影したグリッド数: 1 / 実像数: 3000 / 平均露光時間: 15.0 sec. / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 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): 3.0 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 46730 |
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 |