+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22999 | |||||||||
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タイトル | Negative stain reconstruction of murine antibody M4H2K1 Fab in complex with HIV-1 Env BG505 UFO.664 trimer | |||||||||
マップデータ | full map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 25.0 Å | |||||||||
データ登録者 | Copps J / Ozorowski G / Ward AB | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: mBio / 年: 2021 タイトル: Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. 著者: Sonu Kumar / Xiaohe Lin / Timothy Ngo / Benjamin Shapero / Cindy Sou / Joel D Allen / Jeffrey Copps / Lei Zhang / Gabriel Ozorowski / Linling He / Max Crispin / Andrew B Ward / Ian A Wilson / Jiang Zhu / 要旨: The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and ...The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response. | |||||||||
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_22999.map.gz | 7.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22999-v30.xml emd-22999.xml | 10.1 KB 10.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_22999.png | 58 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22999 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22999 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22999_validation.pdf.gz | 288.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22999_full_validation.pdf.gz | 288.1 KB | 表示 | |
XML形式データ | emd_22999_validation.xml.gz | 5.7 KB | 表示 | |
CIF形式データ | emd_22999_validation.cif.gz | 6.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22999 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22999 | 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_22999.map.gz / 形式: CCP4 / 大きさ: 15.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.05 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 : 3 copies of M4H2K1 Fab in complex with trimeric HIV-1 Env BG505 U...
全体 | 名称: 3 copies of M4H2K1 Fab in complex with trimeric HIV-1 Env BG505 UFO.664 |
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要素 |
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-超分子 #1: 3 copies of M4H2K1 Fab in complex with trimeric HIV-1 Env BG505 U...
超分子 | 名称: 3 copies of M4H2K1 Fab in complex with trimeric HIV-1 Env BG505 UFO.664 タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換株: HEK293F |
分子量 | 理論値: 570 KDa |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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 | 0.01 mg/mL | ||||||
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緩衝液 | pH: 7.4 構成要素:
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染色 | タイプ: NEGATIVE / 材質: uranyl formate / 詳細: 2% (w/v) UF applied for 60 s | ||||||
グリッド | モデル: Homemade / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: PLASMA CLEANING |
-電子顕微鏡法
顕微鏡 | FEI TECNAI SPIRIT |
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撮影 | フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) 平均電子線量: 25.0 e/Å2 |
電子線 | 加速電圧: 120 kV / 電子線源: LAB6 |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 倍率(公称値): 52000 |
試料ステージ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
実験機器 | モデル: Tecnai Spirit / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: 詳細: Map created from PDB coordinates and low pass filtered |
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最終 再構成 | 想定した対称性 - 点群: C3 (3回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 25.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. v2) / 使用した粒子像数: 14027 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |