+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7kjr | |||||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 ORF3a | |||||||||
要素 |
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キーワード | TRANSPORT PROTEIN (運搬体タンパク質) / VIRAL PROTEIN (ウイルスタンパク質) / SARS-CoV-2 (SARSコロナウイルス2) / coronavirus (オルトコロナウイルス亜科) / viroporin / membrane protein (膜タンパク質) | |||||||||
機能・相同性 | 機能・相同性情報 host cell lysosome / induction by virus of host reticulophagy / Maturation of protein 3a / high-density lipoprotein particle receptor binding / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / SARS-CoV-2 modulates autophagy ...host cell lysosome / induction by virus of host reticulophagy / Maturation of protein 3a / high-density lipoprotein particle receptor binding / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / SARS-CoV-2 modulates autophagy / regulation of intestinal cholesterol absorption / negative regulation of response to cytokine stimulus / protein oxidation / vitamin transport / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / positive regulation of phospholipid efflux / high-density lipoprotein particle binding / cholesterol import / Chylomicron assembly / positive regulation of cholesterol metabolic process / negative regulation of heterotypic cell-cell adhesion / high-density lipoprotein particle remodeling / blood vessel endothelial cell migration / ABC transporters in lipid homeostasis / phospholipid efflux / apolipoprotein receptor binding / high-density lipoprotein particle clearance / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / apolipoprotein A-I receptor binding / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / cholesterol transfer activity / reverse cholesterol transport / phosphatidylcholine biosynthetic process / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / lipoprotein biosynthetic process / glucocorticoid metabolic process / positive regulation of CoA-transferase activity / phosphatidylcholine metabolic process / lipid storage / phospholipid homeostasis / high-density lipoprotein particle / triglyceride homeostasis / regulation of Cdc42 protein signal transduction / cholesterol transport / chemorepellent activity / HDL remodeling / cholesterol efflux / Scavenging by Class A Receptors / endothelial cell proliferation / inorganic cation transmembrane transport / cholesterol binding / negative regulation of interleukin-1 beta production / host cell endoplasmic reticulum / positive regulation of Rho protein signal transduction / negative chemotaxis / adrenal gland development / voltage-gated calcium channel complex / cholesterol biosynthetic process / positive regulation of cholesterol efflux / endocytic vesicle / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / voltage-gated potassium channel complex / positive regulation of phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / endocytic vesicle lumen / positive regulation of stress fiber assembly / cholesterol metabolic process / heat shock protein binding / cholesterol homeostasis / molecular function activator activity / integrin-mediated signaling pathway / Post-translational protein phosphorylation / phospholipid binding / regulation of protein phosphorylation / Heme signaling / PPARA activates gene expression / negative regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / : / Platelet degranulation / protein complex oligomerization / monoatomic ion channel activity / amyloid-beta binding / host cell endosome / cytoplasmic vesicle / collagen-containing extracellular matrix / blood microparticle / secretory granule lumen / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion 類似検索 - 分子機能 | |||||||||
生物種 | Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) Homo sapiens (ヒト) | |||||||||
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: 2.08 Å | |||||||||
データ登録者 | Kern, D.M. / Hoel, C.M. / Kotecha, A. / Brohawn, S.G. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2021 タイトル: Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. 著者: David M Kern / Ben Sorum / Sonali S Mali / Christopher M Hoel / Savitha Sridharan / Jonathan P Remis / Daniel B Toso / Abhay Kotecha / Diana M Bautista / Stephen G Brohawn / 要旨: SARS-CoV-2 ORF3a is a putative viral ion channel implicated in autophagy inhibition, inflammasome activation and apoptosis. 3a protein and anti-3a antibodies are found in infected patient tissues and ...SARS-CoV-2 ORF3a is a putative viral ion channel implicated in autophagy inhibition, inflammasome activation and apoptosis. 3a protein and anti-3a antibodies are found in infected patient tissues and plasma. Deletion of 3a in SARS-CoV-1 reduces viral titer and morbidity in mice, suggesting it could be an effective target for vaccines or therapeutics. Here, we present structures of SARS-CoV-2 3a determined by cryo-EM to 2.1-Å resolution. 3a adopts a new fold with a polar cavity that opens to the cytosol and membrane through separate water- and lipid-filled openings. Hydrophilic grooves along outer helices could form ion-conduction paths. Using electrophysiology and fluorescent ion imaging of 3a-reconstituted liposomes, we observe Ca-permeable, nonselective cation channel activity, identify mutations that alter ion permeability and discover polycationic inhibitors of 3a activity. 3a-like proteins are found across coronavirus lineages that infect bats and humans, suggesting that 3a-targeted approaches could treat COVID-19 and other coronavirus diseases. #1: ジャーナル: bioRxiv / 年: 2021 タイトル: Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs. 著者: David M Kern / Ben Sorum / Sonali S Mali / Christopher M Hoel / Savitha Sridharan / Jonathan P Remis / Daniel B Toso / Abhay Kotecha / Diana M Bautista / Stephen G Brohawn / 要旨: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a. 3a is ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma. 3a has been implicated in viral release, inhibition of autophagy, inflammasome activation, and cell death and its deletion reduces viral titer and morbidity in mice, raising the possibility that 3a could be an effective vaccine or therapeutic target. Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 Å resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca-permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multiple and lineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases. | |||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7kjr.cif.gz | 105.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7kjr.ent.gz | 75.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7kjr.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kjr ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kjr | HTTPS FTP |
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-関連構造データ
関連構造データ | 22898MC 6xdcC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10612 (タイトル: High-resolution SARS-CoV-2 ORF3a dimer in an MSP1E3D1 lipid nanodisc Data size: 3.2 TB Data #1: Unaligned movies in EER format of SARS-CoV-2 3a in MSP1E3D1 lipid nanodiscs - 1379 frames [micrographs - multiframe] Data #2: Unaligned movies in EER format of SARS-CoV-2 3a in MSP1E3D1 lipid nanodiscs - 1449 frames [micrographs - multiframe]) |
-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: 32165.902 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) 遺伝子: 3a 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P0DTC3 #2: タンパク質 | 分子量: 24647.678 Da / 分子数: 2 / Fragment: UNP residues 79-267 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APOA1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02647 #3: 化合物 | #4: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | N | |
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-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: SARS-CoV-2 protein 3A in lipid nanodiscsSARSコロナウイルス タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT | |||||||||||||||
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分子量 | 値: 0.062 MDa / 実験値: NO | |||||||||||||||
由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (SARSコロナウイルス2) | |||||||||||||||
由来(組換発現) | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) | |||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 1.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | |||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K / 詳細: 1 blot force 5 second wait time 3 second blot time |
-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 FIELDBright-field microscopy |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) |
-解析
ソフトウェア |
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EMソフトウェア | 名称: PHENIX / バージョン: 1.18.2-3874-000 / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.08 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 91218 / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 42.33 Å2 | ||||||||||||||||||||||||
拘束条件 |
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