+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6adl | ||||||
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タイトル | Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions | ||||||
要素 |
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キーワード | VIRUS / Seneca Valley virus | ||||||
機能・相同性 | 機能・相同性情報 reproductive process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / RNA-protein covalent cross-linking / : / : / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host TRAF-mediated signal transduction ...reproductive process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / RNA-protein covalent cross-linking / : / : / host cell nucleolus / filopodium membrane / adhesion receptor-mediated virion attachment to host cell / negative regulation of extracellular matrix assembly / symbiont-mediated suppression of host TRAF-mediated signal transduction / blood vessel development / lamellipodium membrane / Uptake and function of anthrax toxins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / collagen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / substrate adhesion-dependent cell spreading / picornain 3C / T=pseudo3 icosahedral viral capsid / channel activity / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / monoatomic ion transmembrane transport / transmembrane signaling receptor activity / actin filament binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / actin cytoskeleton organization / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / entry receptor-mediated virion attachment to host cell / RNA helicase activity / endosome membrane / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Senecavirus A (ウイルス) | ||||||
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: 3.08 Å | ||||||
データ登録者 | Lou, Z.Y. / Cao, L. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2018 タイトル: Seneca Valley virus attachment and uncoating mediated by its receptor anthrax toxin receptor 1. 著者: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li ...著者: Lin Cao / Ran Zhang / Tingting Liu / Zixian Sun / Mingxu Hu / Yuna Sun / Lingpeng Cheng / Yu Guo / Sheng Fu / Junjie Hu / Xiangmin Li / Chengqi Yu / Hanyang Wang / Huanchun Chen / Xueming Li / Elizabeth E Fry / David I Stuart / Ping Qian / Zhiyong Lou / Zihe Rao / 要旨: Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here ...Seneca Valley virus (SVV) is an oncolytic picornavirus with selective tropism for neuroendocrine cancers. SVV mediates cell entry by attachment to the receptor anthrax toxin receptor 1 (ANTXR1). Here we determine atomic structures of mature SVV particles alone and in complex with ANTXR1 in both neutral and acidic conditions, as well as empty "spent" particles in complex with ANTXR1 in acidic conditions by cryoelectron microscopy. SVV engages ANTXR1 mainly by the VP2 DF and VP1 CD loops, leading to structural changes in the VP1 GH loop and VP3 GH loop, which attenuate interprotomer interactions and destabilize the capsid assembly. Despite lying on the edge of the attachment site, VP2 D146 interacts with the metal ion in ANTXR1 and is required for cell entry. Though the individual substitution of most interacting residues abolishes receptor binding and virus propagation, a serine-to-alanine mutation at VP2 S177 significantly increases SVV proliferation. Acidification of the SVV-ANTXR1 complex results in a major reconfiguration of the pentameric capsid assemblies, which rotate ∼20° around the icosahedral fivefold axes to form a previously uncharacterized spent particle resembling a potential uncoating intermediate with remarkable perforations at both two- and threefold axes. These structures provide high-resolution snapshots of SVV entry, highlighting opportunities for anticancer therapeutic optimization. | ||||||
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 | 6adl.cif.gz | 172.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6adl.ent.gz | 132.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6adl.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 | 6adl_validation.pdf.gz | 954.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6adl_full_validation.pdf.gz | 963.6 KB | 表示 | |
XML形式データ | 6adl_validation.xml.gz | 30.8 KB | 表示 | |
CIF形式データ | 6adl_validation.cif.gz | 45.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ad/6adl ftp://data.pdbj.org/pub/pdb/validation_reports/ad/6adl | HTTPS FTP |
-関連構造データ
関連構造データ | 9607MC 9608C 9611C 9612C 9613C 6admC 6adrC 6adsC 6adtC 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 |
-リンク
-集合体
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 25785.305 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Senecavirus A (ウイルス) / 参照: UniProt: A0A1I9WAH6*PLUS |
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#2: タンパク質 | 分子量: 26255.791 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Senecavirus A (ウイルス) / 参照: UniProt: A0A1I9WAH6*PLUS |
#3: タンパク質 | 分子量: 27724.059 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Senecavirus A (ウイルス) / 参照: UniProt: Q155Z9*PLUS |
#4: タンパク質 | 分子量: 21316.020 Da / 分子数: 1 / Fragment: UNP residues 38-220 / Mutation: C177A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ANTXR1 / 発現宿主: Enterobacteria phage L1 (ファージ) / 参照: UniProt: Q9H6X2 |
#5: 化合物 | ChemComp-MG / |
研究の焦点であるリガンドがあるか | N |
Has protein modification | Y |
-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: Seneca valley virus / タイプ: VIRUS / Entity ID: #1-#4 / 由来: NATURAL |
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由来(天然) | 生物種: Seneca valley virus (ウイルス) |
ウイルスについての詳細 | 中空か: YES / エンベロープを持つか: NO / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Homo sapiens |
緩衝液 | pH: 6 |
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-PROPANE |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI ARCTICA |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 1.63 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.11.1_2575: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.08 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 3171 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||||||||||||||
拘束条件 |
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