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基本情報
登録情報 | データベース: EMDB / ID: EMD-23229 | |||||||||
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タイトル | BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point) | |||||||||
![]() | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point). Main map | |||||||||
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機能・相同性 | ![]() 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 / structural molecule activity / virion membrane / identical protein binding / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
![]() | Antanasijevic A / Sewall LM / Perrett HR / Ward AB | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. 著者: Aleksandar Antanasijevic / Leigh M Sewall / Christopher A Cottrell / Diane G Carnathan / Luis E Jimenez / Julia T Ngo / Jennifer B Silverman / Bettina Groschel / Erik Georgeson / Jinal Bhiman ...著者: Aleksandar Antanasijevic / Leigh M Sewall / Christopher A Cottrell / Diane G Carnathan / Luis E Jimenez / Julia T Ngo / Jennifer B Silverman / Bettina Groschel / Erik Georgeson / Jinal Bhiman / Raiza Bastidas / Celia LaBranche / Joel D Allen / Jeffrey Copps / Hailee R Perrett / Kimmo Rantalainen / Fabien Cannac / Yuhe R Yang / Alba Torrents de la Peña / Rebeca Froes Rocha / Zachary T Berndsen / David Baker / Neil P King / Rogier W Sanders / John P Moore / Shane Crotty / Max Crispin / David C Montefiori / Dennis R Burton / William R Schief / Guido Silvestri / Andrew B Ward / ![]() ![]() ![]() 要旨: Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate ...Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
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マップデータ | ![]() | 165.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 26.5 KB 26.5 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.8 KB | 表示 | ![]() |
画像 | ![]() | 155.7 KB | ||
マスクデータ | ![]() | 178 MB | ![]() | |
その他 | ![]() ![]() | 140.5 MB 141 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7l8cMC ![]() 7l7tC ![]() 7l7uC ![]() 7l85C ![]() 7l86C ![]() 7l87C ![]() 7l88C ![]() 7l89C ![]() 7l8aC ![]() 7l8bC ![]() 7l8dC ![]() 7l8eC ![]() 7l8fC ![]() 7l8gC ![]() 7l8sC ![]() 7l8tC ![]() 7l8uC ![]() 7l8wC ![]() 7l8xC ![]() 7l8yC ![]() 7l8zC ![]() 7l90C C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point). Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.03 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
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: 3D map of BG505 SOSIP MD39 in complex...
ファイル | emd_23229_half_map_1.map | ||||||||||||
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注釈 | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point). Half-map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: 3D map of BG505 SOSIP MD39 in complex...
ファイル | emd_23229_half_map_2.map | ||||||||||||
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注釈 | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point). Half-map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from a...
全体 | 名称: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point) |
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要素 |
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-超分子 #1: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from a...
超分子 | 名称: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 詳細: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from ...詳細: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from the immune complex dataset using the focused classification approach. |
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由来(天然) | 生物種: ![]() ![]() |
-分子 #1: BG505 SOSIP MD39 - gp120
分子 | 名称: BG505 SOSIP MD39 - gp120 / タイプ: protein_or_peptide / ID: 1 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 52.532418 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...文字列: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNVTNNITDD MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV II RSENITN NAKNILVQLN TPVQINCTRP NNNTVKSIRI GPGQAFYYTG DIIGDIRQAH CNVSKATWNE TLGKVVKQLR KHF GNNTII RFAQSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKR |
-分子 #2: BG505 SOSIP MD39 - gp41
分子 | 名称: BG505 SOSIP MD39 - gp41 / タイプ: protein_or_peptide / ID: 2 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 16.665773 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: VSLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR APEPQQHLLK DTHWGIKQLQ ARVLAVEHYL RDQQLLGIWG CSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD |
-分子 #3: Rh.33104 pAbC-3 - Heavy Chain
分子 | 名称: Rh.33104 pAbC-3 - Heavy Chain / タイプ: protein_or_peptide / ID: 3 詳細: This is a polyclonal antibody and the sequence is inherently unknown. Poly-alanine pseudo-model is used to depict the backbone of this antibody. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 9.634868 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) |
-分子 #4: Rh.33104 pAbC-3 - Light Chain
分子 | 名称: Rh.33104 pAbC-3 - Light Chain / タイプ: protein_or_peptide / ID: 4 詳細: This is a polyclonal antibody and the sequence is inherently unknown. Poly-alanine pseudo-model is used to depict the backbone of this antibody. コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 9.124238 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-分子 #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 8 / コピー数: 17 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 6 mg/mL | |||||||||
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緩衝液 | pH: 7.4 構成要素:
詳細: TBS buffer prepared from a 10X stock | |||||||||
グリッド | モデル: UltrAuFoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING / 前処理 - 雰囲気: OTHER | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV / 詳細: Blotting time varied between 3 and 7 seconds.. | |||||||||
詳細 | Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / デジタル化 - 画像ごとのフレーム数: 1-30 / 撮影したグリッド数: 2 / 実像数: 3194 / 平均露光時間: 7.5 sec. / 平均電子線量: 44.9 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.6 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 29000 |
試料ステージ | 試料ホルダーモデル: OTHER / ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |