- PDB-5npj: Structure of the Hepatitis C virus strain JFH1 glycoprotein E2 an... -
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基本情報
登録情報
データベース: PDB / ID: 5npj
タイトル
Structure of the Hepatitis C virus strain JFH1 glycoprotein E2 antigenic region 532-540 bound to the single chain variable fragment of the non-neutralizing antibody DAO5
要素
Epitope peptide
Single chain variable fragment of the non-neutralizing antibody DAO5
キーワード
VIRAL PROTEIN (ウイルスタンパク質) / Envelope glycoprotein / Hepatitis C virus (C型肝炎ウイルス) / single chain variable fragment (単鎖可変領域フラグメント) / CD81 binding loop
機能・相同性
機能・相同性情報
negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity ...negative regulation of autophagy of mitochondrion / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / negative regulation of autophagy / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ヘリカーゼ / induction by virus of host autophagy / ribonucleoprotein complex / RNA依存性RNAポリメラーゼ / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / タンパク質分解 / RNA binding / zinc ion binding / ATP binding / 生体膜 / identical protein binding 類似検索 - 分子機能
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 抗体 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / サンドイッチ / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta 類似検索 - ドメイン・相同性
A: Single chain variable fragment of the non-neutralizing antibody DAO5 B: Single chain variable fragment of the non-neutralizing antibody DAO5 D: Epitope peptide E: Epitope peptide
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
波長: 1.00004 Å / 相対比: 1
反射
解像度: 1.9→49.23 Å / Num. obs: 58977 / % possible obs: 98.5 % / 冗長度: 4.4 % / Biso Wilson estimate: 19.77 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.5
反射 シェル
解像度: 1.9→2 Å / 冗長度: 4.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 8629 / % possible all: 99.8
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解析
ソフトウェア
名称
バージョン
分類
BUSTER
2.10.2
精密化
XDS
データ削減
XSCALE
データスケーリング
PHASER
位相決定
精密化
構造決定の手法: 分子置換 開始モデル: single chain variable fragment 解像度: 1.9→48.33 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.109 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.103 / SU Rfree Cruickshank DPI: 0.101