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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-21184 | |||||||||
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タイトル | BG505-SOSIP map reconstructed by subparticle extraction and refinement from an icosahedral nanoparticle (I53_dn5) | |||||||||
![]() | BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM map | |||||||||
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生物種 | synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.68 Å | |||||||||
![]() | Ward AB / Antanasijevic A | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens. 著者: Aleksandar Antanasijevic / George Ueda / Philip J M Brouwer / Jeffrey Copps / Deli Huang / Joel D Allen / Christopher A Cottrell / Anila Yasmeen / Leigh M Sewall / Ilja Bontjer / Thomas J ...著者: Aleksandar Antanasijevic / George Ueda / Philip J M Brouwer / Jeffrey Copps / Deli Huang / Joel D Allen / Christopher A Cottrell / Anila Yasmeen / Leigh M Sewall / Ilja Bontjer / Thomas J Ketas / Hannah L Turner / Zachary T Berndsen / David C Montefiori / Per Johan Klasse / Max Crispin / David Nemazee / John P Moore / Rogier W Sanders / Neil P King / David Baker / Andrew B Ward / ![]() ![]() ![]() 要旨: Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and ...Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and geometries enables combination with antigens of choice to test novel multimerization concepts in immunization strategies where the goal is to improve the induction and maturation of neutralizing antibody lineages. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to an underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. When the immunogenicity of ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle or as soluble proteins were compared in rabbits, the two immunogens elicited similar serum antibody binding titers against the trimer component. Neutralizing antibody titers were slightly elevated in the animals given the nanoparticle immunogen and were initially more focused to the trimer apex. Altogether, our findings indicate that tetrahedral nanoparticles can be successfully applied for presentation of HIV Env trimer immunogens; however, the optimal implementation to different immunization strategies remains to be determined. | |||||||||
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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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-EMDBアーカイブ
マップデータ | ![]() | 20 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 21.4 KB 21.4 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 6.5 KB | 表示 | ![]() |
画像 | ![]() | 55.8 KB | ||
マスクデータ | ![]() | 22.2 MB | ![]() | |
その他 | ![]() ![]() | 16.9 MB 16.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 78.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 77.3 KB | 表示 | |
XML形式データ | ![]() | 494 B | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.15 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: BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53 dn5 nanoparticle,...
ファイル | emd_21184_half_map_1.map | ||||||||||||
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注釈 | BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM 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: BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53 dn5 nanoparticle,...
ファイル | emd_21184_half_map_2.map | ||||||||||||
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注釈 | BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM 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 reconstructed from the icosahedral nanoparticle I53_d...
全体 | 名称: BG505-SOSIP reconstructed from the icosahedral nanoparticle I53_dn5 by subparticle extraction and refinement |
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要素 |
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-超分子 #1: BG505-SOSIP reconstructed from the icosahedral nanoparticle I53_d...
超分子 | 名称: BG505-SOSIP reconstructed from the icosahedral nanoparticle I53_dn5 by subparticle extraction and refinement タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: Nanoparticle is assembled by combining equimolar amounts of BG505-SOSIP-I53_dn5B and I53_dn5A and subsequent incubation. EM map of the full nanoparticle can be found elsewhere (D_1000246150). |
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由来(天然) | 生物種: synthetic construct (人工物) |
-分子 #1: BG505-SOSIP-I53_dn5B
分子 | 名称: BG505-SOSIP-I53_dn5B / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: synthetic construct (人工物) |
組換発現 | 生物種: ![]() |
配列 | 文字列: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF ...文字列: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CTNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVIIRSENIT NNAKNILVQL NESVQINCTR PNNNTVKSIR IGPGQWFYYT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAVGIGAV SLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PECQQHLLKD THWGIKQLQA RVLAVEHYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ GSGSGSGSGG EEAELAYLLG ELAYKLGEYR IAIRAYRIAL KRDPNNAEAW YNLGNAYYKQ GRYREAIEYY QKALELDPNN AEAWYNLGNA YYERGEYEEA IEYYRKALRL DPNNADAMQN LLNAKMREEL EAS |
-分子 #2: I53_dn5A
分子 | 名称: I53_dn5A / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: synthetic construct (人工物) |
配列 | 文字列: MGKYDGSKLR IGILHARWNA EIILALVLGA LKRLQEFGVK RENIIIETVP GSFELPYGSK LFVEKQKRLG KPLDAIIPIG VLIKGSTMHF EYICDSTTHQ LMKLNFELGI PVIFGVLTCL TDEQAEARAG LIEGKMHNHG EDWGAAAVEM ATKFNLEHHH HHH |
-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 | 1.7 mg/mL | |||||||||
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緩衝液 | pH: 7.4 構成要素:
詳細: TBS buffer, pH 7.4 | |||||||||
グリッド | モデル: Quantifoil R2/1 / 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: HOLEY / 支持フィルム - Film thickness: 11.0 nm / 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 in the 3-7 s range, Blotting force set to 0, Wait time of 10s.. | |||||||||
詳細 | Nanoparticle is assembled by combining equimolar amounts of BG505-SOSIP-I53_dn5B and I53_dn5A and subsequent incubation. Nanoparticle is purified from unassembled components by SEC. Sample is then concentrated to 1.7mg/ml in TBS buffer. |
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電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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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 / 撮影したグリッド数: 2 / 実像数: 2999 / 平均露光時間: 11.25 sec. / 平均電子線量: 49.39 e/Å2 |
電子線 | 加速電圧: 200 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): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 36000 |
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: Talos Arctica / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
詳細 | Model refinement was not performed due to low resolution. |
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