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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: PDB / ID: 8err | ||||||
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タイトル | SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 Omicron variant / COVID-19 / spike glycoprotein / fusion protein / neutralizing antibodies / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / inhibitor / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
機能・相同性 | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
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: 3.1 Å | ||||||
![]() | Park, Y.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. 著者: Young-Jun Park / Dora Pinto / Alexandra C Walls / Zhuoming Liu / Anna De Marco / Fabio Benigni / Fabrizia Zatta / Chiara Silacci-Fregni / Jessica Bassi / Kaitlin R Sprouse / Amin Addetia / ...著者: Young-Jun Park / Dora Pinto / Alexandra C Walls / Zhuoming Liu / Anna De Marco / Fabio Benigni / Fabrizia Zatta / Chiara Silacci-Fregni / Jessica Bassi / Kaitlin R Sprouse / Amin Addetia / John E Bowen / Cameron Stewart / Martina Giurdanella / Christian Saliba / Barbara Guarino / Michael A Schmid / Nicholas M Franko / Jennifer K Logue / Ha V Dang / Kevin Hauser / Julia di Iulio / William Rivera / Gretja Schnell / Anushka Rajesh / Jiayi Zhou / Nisar Farhat / Hannah Kaiser / Martin Montiel-Ruiz / Julia Noack / Florian A Lempp / Javier Janer / Rana Abdelnabi / Piet Maes / Paolo Ferrari / Alessandro Ceschi / Olivier Giannini / Guilherme Dias de Melo / Lauriane Kergoat / Hervé Bourhy / Johan Neyts / Leah Soriaga / Lisa A Purcell / Gyorgy Snell / Sean P J Whelan / Antonio Lanzavecchia / Herbert W Virgin / Luca Piccoli / Helen Y Chu / Matteo Samuele Pizzuto / Davide Corti / David Veesler / ![]() ![]() ![]() ![]() ![]() 要旨: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 680.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 526.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 98.8 KB | 表示 | |
CIF形式データ | ![]() | 154 KB | 表示 | |
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 | ![]() 28559MC ![]() 8erqC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 141870.719 Da / 分子数: 3 / 由来タイプ: 組換発現 詳細: Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike ...詳細: Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein,Omicron BA.1 spike glycoprotein 由来: (組換発現) ![]() ![]() 遺伝子: S, 2 / 発現宿主: ![]() #2: 抗体 | 分子量: 13201.017 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #3: 抗体 | 分子量: 11513.587 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 糖 | ChemComp-NAG / 研究の焦点であるリガンドがあるか | N | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 |
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試料調製
構成要素 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 60 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 537649 / 対称性のタイプ: POINT |