+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1182 | |||||||||
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タイトル | Structural and functional insights into the interaction of echoviruses and decay-accelerating factor. | |||||||||
マップデータ | Reconstruction of Echovirus type 12 bound to Decay Accelerating Factor. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / virus receptor activity / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / DNA replication / RNA helicase activity / membrane raft / induction by virus of host autophagy / Golgi membrane / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / innate immune response / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human echovirus 12 (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / ネガティブ染色法 / 解像度: 16.0 Å | |||||||||
データ登録者 | Pettigrew DM / Williams DT / Kerrigan D / Evans DJ / Lea SM / Bhella D | |||||||||
引用 | ジャーナル: J Biol Chem / 年: 2006 タイトル: Structural and functional insights into the interaction of echoviruses and decay-accelerating factor. 著者: David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella / 要旨: Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo- ...Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo-negative stain transmission electron microscopy and three-dimensional image reconstruction to 16-A resolution, which we interpreted using the atomic structures of EV11 and DAF. DAF binds to a hypervariable region of the capsid close to the 2-fold symmetry axes in an interaction that involves mostly the short consensus repeat 3 domain of DAF and the capsid protein VP2. A bulge in the density for the short consensus repeat 3 domain suggests that a loop at residues 174-180 rearranges to prevent steric collision between closely packed molecules at the 2-fold symmetry axes. Detailed analysis of receptor interactions between a variety of echoviruses and DAF using surface plasmon resonance and comparison of this structure (and our previous work; Bhella, D., Goodfellow, I. G., Roversi, P., Pettigrew, D., Chaudhry, Y., Evans, D. J., and Lea, S. M. (2004) J. Biol. Chem. 279, 8325-8332) with reconstructions published for EV7 bound to DAF support major differences in receptor recognition among these viruses. However, comparison of the electron density for the two virus.receptor complexes (rather than comparisons of the pseudo-atomic models derived from fitting the coordinates into these densities) suggests that the dramatic differences in interaction affinities/specificities may arise from relatively subtle structural differences rather than from large-scale repositioning of the receptor with respect to the virus surface. | |||||||||
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_1182.map.gz | 12.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1182-v30.xml emd-1182.xml | 11.1 KB 11.1 KB | 表示 表示 | EMDBヘッダ |
画像 | 1182.gif emd_1182.tif | 33.8 KB 28.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1182 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1182 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_1182_validation.pdf.gz | 222.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_1182_full_validation.pdf.gz | 221.6 KB | 表示 | |
XML形式データ | emd_1182_validation.xml.gz | 6.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1182 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1182 | 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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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_1182.map.gz / 形式: CCP4 / 大きさ: 61.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of Echovirus type 12 bound to Decay Accelerating Factor. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.18 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 : Echovirus type 12 bound to decay accelerating factor
全体 | 名称: Echovirus type 12 bound to decay accelerating factor |
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要素 |
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-超分子 #1000: Echovirus type 12 bound to decay accelerating factor
超分子 | 名称: Echovirus type 12 bound to decay accelerating factor タイプ: sample / ID: 1000 / 集合状態: Sixty DAF molecules binds to one virion. / Number unique components: 2 |
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-超分子 #1: Human echovirus 12
超分子 | 名称: Human echovirus 12 / タイプ: virus / ID: 1 / Name.synonym: EV12 / NCBI-ID: 35293 / 生物種: Human echovirus 12 / ウイルスタイプ: VIRION / ウイルス・単離状態: SEROTYPE / ウイルス・エンベロープ: No / ウイルス・中空状態: No / Syn species name: EV12 |
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宿主 | 生物種: Homo sapiens (ヒト) / 別称: VERTEBRATES |
ウイルス殻 | Shell ID: 1 / 名称: VP1-4 / 直径: 300 Å / T番号(三角分割数): 3 |
-超分子 #2: Decay accelerating factor short consensus repeat domains one to four
超分子 | 名称: Decay accelerating factor short consensus repeat domains one to four タイプ: organelle_or_cellular_component / ID: 2 / Name.synonym: DAF / コピー数: 60 / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: human / 細胞中の位置: plasma membrane |
組換発現 | 生物種: Komagataella pastoris (菌類) |
-実験情報
-構造解析
手法 | ネガティブ染色法, 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 | 0.2 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: Phosphate buffered saline |
染色 | タイプ: NEGATIVE 詳細: 5 microlitres of sample was loaded onto a quantifoil grid and then floated on a 20 microlitre droplet of 15% Ammonium Molybdate for 10 seconds, then the grid was blotted for 2 seconds before ...詳細: 5 microlitres of sample was loaded onto a quantifoil grid and then floated on a 20 microlitre droplet of 15% Ammonium Molybdate for 10 seconds, then the grid was blotted for 2 seconds before vitrification in liquid ethane. |
グリッド | 詳細: 400 mesh R2/2 quantifoils |
凍結 | 凍結剤: ETHANE / 手法: Blot for two seconds, wait for two seconds. |
-電子顕微鏡法
顕微鏡 | JEOL 1200 |
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温度 | 平均: 100 K |
アライメント法 | Legacy - 非点収差: Objective astigmatism corrected at 200,000 times mag |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: NIKON COOLSCAN / デジタル化 - サンプリング間隔: 6.35 µm / 実像数: 192 / 詳細: Scanned on Nikon Coolscan / ビット/ピクセル: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
電子線 | 加速電圧: 120 kV / 電子線源: LAB6 |
電子光学系 | 倍率(補正後): 29100 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 3.4 mm / 最大 デフォーカス(公称値): 2.8 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 30000 |
試料ステージ | 試料ホルダー: Side entry liquid-nitrogen cooled / 試料ホルダーモデル: OTHER |
-画像解析
CTF補正 | 詳細: defocus pairs, each particle - CTFmix |
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最終 再構成 | 想定した対称性 - 点群: I (正20面体型対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 16.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: PFT2 and EM3DR2 / 使用した粒子像数: 1339 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: E |
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詳細 | Protocol: search using known inter-domain orientations. based on earlier EV12/DAF34 fits using known inter-domain angles from the DAF1234 crystal structures. |
精密化 | 空間: REAL / 温度因子: 95 / 当てはまり具合の基準: correlation coefficient |
得られたモデル | PDB-2c8i: |