+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1upn | ||||||
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タイトル | COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A | ||||||
要素 |
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キーワード | VIRUS/RECEPTOR / COMPLEX (VIRUS COAT-IMMUNE PROTEIN) / ECHOVIRUS / PICORNAVIRUS / CD55 / DAF / VIRUS-RECEPTOR COMPLEX / ICOSAHEDRAL VIRUS | ||||||
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 / 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 / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) HUMAN ECHOVIRUS 11 (ウイルス) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / クライオ電子顕微鏡法 / 解像度: 16 Å | ||||||
データ登録者 | Bhella, D. / Goodfellow, I.G. / Roversi, P. / Pettigrew, D. / Chaudry, Y. / Evans, D.J. / Lea, S.M. | ||||||
引用 | ジャーナル: J Biol Chem / 年: 2004 タイトル: The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55). 著者: David Bhella / Ian G Goodfellow / Pietro Roversi / David Pettigrew / Yasmin Chaudhry / David J Evans / Susan M Lea / 要旨: Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three- ...Echovirus type 12 (EV12), an Enterovirus of the Picornaviridae family, uses the complement regulator decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF consisting of short consensus repeat domains 3 and 4 from cryo-negative stain electron microscopy data (EMD code 1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the 2-fold symmetry axes. Despite this general similarity our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF(34) and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB code 1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF binding phenotype in these viruses. | ||||||
履歴 |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-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 | 1upn.cif.gz | 171.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1upn.ent.gz | 136.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1upn.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 | 1upn_validation.pdf.gz | 734.4 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1upn_full_validation.pdf.gz | 775.2 KB | 表示 | |
XML形式データ | 1upn_validation.xml.gz | 35.8 KB | 表示 | |
CIF形式データ | 1upn_validation.cif.gz | 52.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/up/1upn ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upn | 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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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: 32786.668 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: Q8JKE8 |
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#2: タンパク質 | 分子量: 29048.549 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: Q8JKE8 |
#3: タンパク質 | 分子量: 25897.391 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: Q8JKE8 |
#4: タンパク質 | 分子量: 7509.299 Da / 分子数: 1 / 由来タイプ: 天然 詳細: STRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057 由来: (天然) HUMAN ECHOVIRUS 11 (ウイルス) / 株: GREGORY / 参照: UniProt: Q8JKE8 |
#5: タンパク質 | 分子量: 14094.727 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P08174 |
配列の詳細 | THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE ...THE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12 |
-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: ECHOVIRUS TYPE 12 / タイプ: VIRUS |
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緩衝液 | 名称: AMMONIUM MOLYBDATE / pH: 7.4 / 詳細: AMMONIUM MOLYBDATE |
試料 | 濃度: 0.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: YES |
染色 | タイプ: NEGATIVE / 染色剤: Ammonium Molybdate |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 凍結剤: ETHANE / 詳細: LIQUID ETHANE |
結晶化 | *PLUS 手法: 電子顕微鏡法 / 詳細: electron microscopy |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2000EXII / 日付: 2002年7月15日 / 詳細: PARTICLES SELECTED WITH X3D |
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電子銃 | 電子線源: LAB6 / 加速電圧: 120 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 30000 X / 倍率(補正後): 29200 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 300 nm / Cs: 3.4 mm |
試料ホルダ | 温度: 108 K |
撮影 | 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: 16 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア | 名称: MRC IMAGE PROCESSING PACKAGE / カテゴリ: 3次元再構成 | ||||||||||||
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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 / 解像度: 16 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 903 詳細: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS ...詳細: MAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL / Target criteria: Cross-correlation coefficient / 詳細: REFINEMENT PROTOCOL--X-RAY | ||||||||||||
原子モデル構築 | PDB-ID: 1UPN | ||||||||||||
精密化 | 最高解像度: 16 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 16 Å
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