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基本情報
登録情報 | データベース: PDB / ID: 1z7z | |||||||||
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タイトル | Cryo-em structure of human coxsackievirus A21 complexed with five domain icam-1kilifi | |||||||||
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![]() | Virus/Receptor / ICAM-1 / Kilifi / CD54 / Human Coxsackievirus A21 / virus-receptor complex / Icosahedral virus | |||||||||
機能・相同性 | ![]() 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 / adhesion of symbiont to host / establishment of endothelial barrier / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...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 / 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 / ribonucleoside triphosphate phosphatase activity / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / transmembrane signaling receptor activity / integrin binding / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / signaling receptor activity / DNA replication / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / positive regulation of ERK1 and ERK2 cascade / RNA helicase activity / receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / cell adhesion / membrane raft / induction by virus of host autophagy / external side of plasma membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / focal adhesion / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / cell surface / 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 | ![]() ![]() | |||||||||
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: 8 Å | |||||||||
![]() | Xiao, C. / Bator-Kelly, C.M. / Rieder, E. / Chipman, P.R. / Craig, A. / Kuhn, R.J. / Wimmer, E. / Rossmann, M.G. | |||||||||
![]() | ![]() タイトル: The crystal structure of coxsackievirus A21 and its interaction with ICAM-1. 著者: Chuan Xiao / Carol M Bator-Kelly / Elizabeth Rieder / Paul R Chipman / Alister Craig / Richard J Kuhn / Eckard Wimmer / Michael G Rossmann / ![]() 要旨: CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human ...CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 A resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 A resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1(Kilifi). The cryo-EM map was fitted with the crystal structures of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1. | |||||||||
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 | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 206.8 KB | 表示 | ![]() |
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その他 | ![]() |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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対称性 | 点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称)) |
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要素
-Human coxsackievirus ... , 5種, 5分子 12345
#1: タンパク質 | 分子量: 31946.727 Da / 分子数: 1 / 断片: Viral Protein 1 residues 1073-1286 / 由来タイプ: 天然 / 詳細: THE NATURE HOST OF THIS VIRUS IS HUMAN 由来: (天然) ![]() 属: Enterovirus / 細胞株: Hela / 生物種: Human enterovirus C / 株: KUYKENDALL / 参照: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
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#2: タンパク質 | 分子量: 29918.537 Da / 分子数: 1 / 断片: Viral Protein 2 residues 2010-2272 / 由来タイプ: 天然 / 詳細: THE NATURE HOST OF THIS VIRUS IS HUMAN 由来: (天然) ![]() 属: Enterovirus / 細胞株: Hela / 生物種: Human enterovirus C / 株: KUYKENDALL / 参照: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
#3: タンパク質 | 分子量: 25898.895 Da / 分子数: 1 / 断片: Viral Protein 3 residues 3043-3234 / 由来タイプ: 天然 / 詳細: THE NATURE HOST OF THIS VIRUS IS HUMAN 由来: (天然) ![]() 属: Enterovirus / 細胞株: Hela / 生物種: Human enterovirus C / 株: KUYKENDALL / 参照: GenBank: 33304569, UniProt: Q7T7N6*PLUS |
#4: タンパク質・ペプチド | 分子量: 1335.565 Da / 分子数: 1 / 断片: Viral Protein 1 residues 1287-1298 / 由来タイプ: 天然 / 詳細: THE NATURE HOST OF THIS VIRUS IS HUMAN 由来: (天然) ![]() 属: Enterovirus / 細胞株: Hela / 生物種: Human enterovirus C / 株: KUYKENDALL / 参照: GenBank: 33304569, UniProt: P22055*PLUS |
#5: タンパク質・ペプチド | 分子量: 687.809 Da / 分子数: 1 / 断片: Viral Protein 3 residues 3035-3239 / 由来タイプ: 天然 / 詳細: THE NATURE HOST OF THIS VIRUS IS HUMAN 由来: (天然) ![]() 属: Enterovirus / 細胞株: Hela / 生物種: Human enterovirus C / 株: KUYKENDALL / 参照: GenBank: 33304569 |
-タンパク質 / 糖 , 2種, 9分子 I![](data/chem/img/NAG.gif)
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#6: タンパク質 | 分子量: 49104.473 Da / 分子数: 1 / 断片: ICAM-1 EXTRACELLULAR DOMAIN 1-5 / Mutation: K29M / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#7: 糖 | ChemComp-NAG / |
-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 |
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試料調製
構成要素 |
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ウイルスについての詳細 | ホストのカテゴリ: MAMMALIAN / タイプ: VIRION | ||||||||||||||||||||||||||||||||||||||||
天然宿主 | 生物種: Homo sapiens / 株: Hela | ||||||||||||||||||||||||||||||||||||||||
緩衝液 | 名称: TRIS / pH: 7.2 / 詳細: TRIS | ||||||||||||||||||||||||||||||||||||||||
試料 | 濃度: 5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||
試料支持 | 詳細: HOLEY CARBON | ||||||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: REICHERT-JUNG PLUNGER / 凍結剤: ETHANE / 詳細: PLUNGED INTO ETHANE AT LIQUID NITROGEN TEMPERATURE |
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電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T / 日付: 2001年3月15日 詳細: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE. |
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電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 45000 X / 倍率(補正後): 47000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 700 nm / Cs: 2 mm |
試料ホルダ | 温度: 100 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 26 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
画像スキャン | デジタル画像の数: 33 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: REVERSED CTF WITH WEINER FACTOR FOR EACH PARTICLE | ||||||||||||
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
3次元再構成 | 手法: POLAR FOURIER TRANSFORM METHOD AND FOURIER-BESSEL RECONSTRUCTION 解像度: 8 Å / 粒子像の数: 4704 / ピクセルサイズ(公称値): 2.98 Å / ピクセルサイズ(実測値): 2.85 Å 倍率補正: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS ...倍率補正: THE PIXEL SIZE OF THE CRYO-EM MAP WAS CALIBRATED AGAINST THE ATOMIC MODEL OF THE VIRUS CAPSID. DENSITIES WERE COMPARED BY CROSS- CORRELATION WITHIN A SPHERICAL SHELL OF INTERNAL RADIUS 104 ANGSTROMS AND EXTERNAL RADIUS 177 ANGSTROMS. 詳細: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF THE ...詳細: A B-FACTOR OF 589.46 WAS SET FOR ALL THE ATOMS BASED ON THE EQUATION OF -4*LN(0.1*RESOLUTION2) TO MIMIC A 8 ANGSTROM RESOLUTION CRYOEM STRUCTURE. OCCUPANCY OF 1.0 WAS SET FOR ALL ATOMS OF THE VIRAL CAPSID. OCCUPANCY OF 0.80, 0.56, 0.24, 0.16, AND 0.08 WAS SET FOR ATOMS OF ICAM-1 DOMAIN 1, 2, 3, 4, AND 5, RESPECTIVELY, BASED ON THE FITTING RESULTS. SEE DETAILS IN THE CITATION. 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL Target criteria: BEST SUMF VALUE FIT USING THE PROGRAM EMFIT 詳細: REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
原子モデル構築 |
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精密化 | 最高解像度: 8 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 8 Å
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