+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jau | ||||||
---|---|---|---|---|---|---|---|
タイトル | The cryoEM map of EV71 mature viron in complex with the Fab fragment of antibody D5 | ||||||
要素 |
| ||||||
キーワード | VIRUS/IMMUNE SYSTEM / Enterovirus 71(EV71) / virus-antibody complex / bivalent binding / high resolution cryo-EM / VIRUS-IMMUNE SYSTEM complex | ||||||
機能・相同性 | 機能・相同性情報 symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / 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 / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | Human enterovirus (エンテロウイルス) Mus musculus (ハツカネズミ) | ||||||
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: 4.8 Å | ||||||
データ登録者 | Fan, C. / Ye, X.H. / Ku, Z.Q. / Zuo, T. / Kong, L.L. / Zhang, C. / Shi, J.P. / Liu, Q.W. / Chen, T. / Zhang, Y.Y. ...Fan, C. / Ye, X.H. / Ku, Z.Q. / Zuo, T. / Kong, L.L. / Zhang, C. / Shi, J.P. / Liu, Q.W. / Chen, T. / Zhang, Y.Y. / Jiang, W. / Zhang, L.Q. / Huang, Z. / Cong, Y. | ||||||
引用 | ジャーナル: PLoS Pathog / 年: 2016 タイトル: Structural Basis for Recognition of Human Enterovirus 71 by a Bivalent Broadly Neutralizing Monoclonal Antibody. 著者: Xiaohua Ye / Chen Fan / Zhiqiang Ku / Teng Zuo / Liangliang Kong / Chao Zhang / Jinping Shi / Qingwei Liu / Tan Chen / Yingyi Zhang / Wen Jiang / Linqi Zhang / Zhong Huang / Yao Cong / 要旨: Enterovirus 71 (EV71) is the main pathogen responsible for hand, foot and mouth disease with severe neurological complications and even death in young children. We have recently identified a highly ...Enterovirus 71 (EV71) is the main pathogen responsible for hand, foot and mouth disease with severe neurological complications and even death in young children. We have recently identified a highly potent anti-EV71 neutralizing monoclonal antibody, termed D5. Here we investigated the structural basis for recognition of EV71 by the antibody D5. Four three-dimensional structures of EV71 particles in complex with IgG or Fab of D5 were reconstructed by cryo-electron microscopy (cryo-EM) single particle analysis all at subnanometer resolutions. The most critical EV71 mature virion-Fab structure was resolved to a resolution of 4.8 Å, which is rare in cryo-EM studies of virus-antibody complex so far. The structures reveal a bivalent binding pattern of D5 antibody across the icosahedral 2-fold axis on mature virion, suggesting that D5 binding may rigidify virions to prevent their conformational changes required for subsequent RNA release. Moreover, we also identified that the complementary determining region 3 (CDR3) of D5 heavy chain directly interacts with the extremely conserved VP1 GH-loop of EV71, which was validated by biochemical and virological assays. We further showed that D5 is indeed able to neutralize a variety of EV71 genotypes and strains. Moreover, D5 could potently confer protection in a mouse model of EV71 infection. Since the conserved VP1 GH-loop is involved in EV71 binding with its uncoating receptor, the scavenger receptor class B, member 2 (SCARB2), the broadly neutralizing ability of D5 might attribute to its inhibition of EV71 from binding SCARB2. Altogether, our results elucidate the structural basis for the binding and neutralization of EV71 by the broadly neutralizing antibody D5, thereby enhancing our understanding of antibody-based protection against EV71 infection. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 3jau.cif.gz | 55.9 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3jau.ent.gz | 38.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3jau.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 | 3jau_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 3jau_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 3jau_validation.xml.gz | 16.7 KB | 表示 | |
CIF形式データ | 3jau_validation.cif.gz | 22.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jau ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jau | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
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・ペプチド | 分子量: 2001.133 Da / 分子数: 1 / 断片: UNP residues 207-223 / 由来タイプ: 天然 由来: (天然) Human enterovirus (エンテロウイルス) 参照: UniProt: X2L816, UniProt: Q5DW45*PLUS |
---|---|
#2: 抗体 | 分子量: 13026.259 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus |
#3: 抗体 | 分子量: 12112.521 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus |
Has protein modification | Y |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: EV71 mature viron in complex with the Fab fragment of antibody D5 タイプ: COMPLEX 詳細: One fab fragment of antibody D5 bind to one protomer of EV71 |
---|---|
分子量 | 値: 8 MDa / 実験値: NO |
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 / ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Homo sapiens |
緩衝液 | pH: 7.6 / 詳細: 0.15 M phosphate buffered saline(PBS) buffer |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: 0.15 M phosphate buffered saline(PBS) buffer (Stain Details Grids were plunge-frozen into liquid ethane using a FEI Mark IV virtobot, after 2s blotting to remove extra sample.) |
試料支持 | 詳細: 200 mesh R1.2x1.3 Quantifoil Cu grid, glow discharged in air |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / Temp: 120 K / 湿度: 100 % / 手法: Blot for 2 seconds before plunging |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2014年10月2日 |
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): 37000 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 2000 nm / Cs: 0.005 mm 非点収差: Objective lens astigmatism was corrected at 75000 magnification カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER 温度: 91 K / 最高温度: 92 K / 最低温度: 90 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 16 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: 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: common lines / 解像度: 4.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 2902 詳細: (Single particle details: The particles were boxed using e2boxer.py. CTF fitting was automatically performed using fitctf2.py in jspr, then visually validated and adjusted using EMAN1.9 ctfit ...詳細: (Single particle details: The particles were boxed using e2boxer.py. CTF fitting was automatically performed using fitctf2.py in jspr, then visually validated and adjusted using EMAN1.9 ctfit program. The gold standard 3D reconstruction procedure was followed using jspr package, with the datasets split into two halves in the beginning.) (Single particle--Applied symmetry: I) Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 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 / 詳細: REFINEMENT PROTOCOL--rigid body | ||||||||||||
原子モデル構築 | PDB-ID: 3VBS PDB chain-ID: D / Accession code: 3VBS / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
|