+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7bg7 | ||||||
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タイトル | HRV14 in complex with its receptor ICAM-1 | ||||||
要素 |
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キーワード | VIRUS / enterovirus / rhinovirus 14 / HRV14 / RV14 / native particle / receptor / virus-receptor complex / ICAM-1 | ||||||
機能・相同性 | 機能・相同性情報 regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier ...regulation of leukocyte mediated cytotoxicity / T cell extravasation / positive regulation of cellular extravasation / regulation of ruffle assembly / T cell antigen processing and presentation / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / membrane to membrane docking / lysis of host organelle involved in viral entry into host cell / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / leukocyte migration / Interleukin-10 signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunological synapse / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / cellular response to leukemia inhibitory factor / cellular response to glucose stimulus / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cellular response to amyloid-beta / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / integrin binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / signaling receptor activity / symbiont-mediated suppression of host gene expression / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / DNA replication / RNA helicase activity / receptor-mediated virion attachment to host cell / positive regulation of ERK1 and ERK2 cascade / cell adhesion / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / external side of plasma membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / focal adhesion / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Human rhinovirus 14 (ライノウイルス) | ||||||
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: 2.4 Å | ||||||
データ登録者 | Hrebik, D. / Fuzik, T. / Plevka, P. | ||||||
資金援助 | チェコ, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2021 タイトル: ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. 著者: Dominik Hrebík / Tibor Füzik / Mária Gondová / Lenka Šmerdová / Athanassios Adamopoulos / Ondrej Šedo / Zbyněk Zdráhal / Pavel Plevka / 要旨: Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to ...Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14-ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA-VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid-RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release. | ||||||
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 | 7bg7.cif.gz | 181.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7bg7.ent.gz | 143.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7bg7.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 | 7bg7_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7bg7_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 7bg7_validation.xml.gz | 48.6 KB | 表示 | |
CIF形式データ | 7bg7_validation.cif.gz | 72.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/bg/7bg7 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/7bg7 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 5種, 5分子 1234B
#1: タンパク質 | 分子量: 32975.004 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Human rhinovirus 14 (ライノウイルス) 参照: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: タンパク質 | 分子量: 28501.361 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Human rhinovirus 14 (ライノウイルス) 参照: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: タンパク質 | 分子量: 26236.754 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Human rhinovirus 14 (ライノウイルス) 参照: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: タンパク質 | 分子量: 7183.863 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Human rhinovirus 14 (ライノウイルス) 参照: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#5: タンパク質 | 分子量: 49552.004 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ICAM1 / プラスミド: bacmid / Cell (発現宿主): SF9 発現宿主: Baculovirus expression vector pFastBac1-HM (ウイルス) 参照: UniProt: P05362 |
-非ポリマー , 1種, 445分子
#6: 水 | ChemComp-HOH / |
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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 |
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分子量 | 値: 10.0 MDa / 実験値: NO | |||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: Baculovirus expression vector pFastBac1-HM (ウイルス) | |||||||||||||||||||||||||
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 | |||||||||||||||||||||||||
ウイルス殻 | 名称: HRV14-ICAM-1 complex / 直径: 325 nm / 三角数 (T数): 3 | |||||||||||||||||||||||||
緩衝液 | pH: 7.4 / 詳細: PBS | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.5 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: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/1 | |||||||||||||||||||||||||
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: 279.15 K |
-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 / 倍率(公称値): 75000 X / 最大 デフォーカス(公称値): 2400 nm / 最小 デフォーカス(公称値): 500 nm / Calibrated defocus min: 420 nm / 最大 デフォーカス(補正後): 3562 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: ZEMLIN TABLEAU |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 1 sec. / 電子線照射量: 83.6 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) 撮影したグリッド数: 1 / 実像数: 4680 |
画像スキャン | 横: 4096 / 縦: 4096 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 36638 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 12085 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 9.19 / プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 4RHV |