+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7swo | ||||||
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タイトル | C98C7 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) | ||||||
要素 |
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キーワード | VIRAL PROTEIN/Immune System / antibody / virus / immunity / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||
機能・相同性 | 機能・相同性情報 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 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) Homo sapiens (ヒト) | ||||||
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: 4.1 Å | ||||||
データ登録者 | Windsor, I.W. / Tong, P. / Wesemann, D.R. / Harrison, S.C. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Sci Immunol / 年: 2022 タイトル: Antibodies induced by an ancestral SARS-CoV-2 strain that cross-neutralize variants from Alpha to Omicron BA.1. 著者: Ian W Windsor / Pei Tong / Olivia Lavidor / Ali Sanjari Moghaddam / Lindsay G A McKay / Avneesh Gautam / Yuezhou Chen / Elizabeth A MacDonald / Duck Kyun Yoo / Anthony Griffths / Duane R ...著者: Ian W Windsor / Pei Tong / Olivia Lavidor / Ali Sanjari Moghaddam / Lindsay G A McKay / Avneesh Gautam / Yuezhou Chen / Elizabeth A MacDonald / Duck Kyun Yoo / Anthony Griffths / Duane R Wesemann / Stephen C Harrison / 要旨: Neutralizing antibodies that recognize the SARS-CoV-2 spike glycoprotein are the principal host defense against viral invasion. Variants of SARS-CoV-2 bear mutations that allow escape from ...Neutralizing antibodies that recognize the SARS-CoV-2 spike glycoprotein are the principal host defense against viral invasion. Variants of SARS-CoV-2 bear mutations that allow escape from neutralization by many human antibodies, especially those in widely distributed ("public") classes. Identifying antibodies that neutralize these variants of concern and determining their prevalence are important goals for understanding immune protection. To determine the Delta and Omicron BA.1 variant specificity of B cell repertoires established by an initial Wuhan strain infection, we measured neutralization potencies of 73 antibodies from an unbiased survey of the early memory B cell response. Antibodies recognizing each of three previously defined epitopic regions on the spike receptor binding domain (RBD) varied in neutralization potency and variant-escape resistance. The ACE2 binding surface ("RBD-2") harbored the binding sites of neutralizing antibodies with the highest potency but with the greatest sensitivity to viral escape; two other epitopic regions on the RBD ("RBD-1" and "RBD-3") bound antibodies of more modest potency but greater breadth. The structures of several Fab:spike complexes that neutralized all five variants of concern tested, including one Fab each from the RBD-1, -2, and -3 clusters, illustrated the determinants of broad neutralization and showed that B cell repertoires can have specificities that avoid immune escape driven by public antibodies. The structure of the RBD-2 binding, broad neutralizer shows why it retains neutralizing activity for Omicron BA.1, unlike most others in the same public class. Our results correlate with real-world data on vaccine efficacy, which indicate mitigation of disease caused by Omicron BA.1. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7swo.cif.gz | 113.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7swo.ent.gz | 89.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7swo.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 | 7swo_validation.pdf.gz | 662.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7swo_full_validation.pdf.gz | 681 KB | 表示 | |
XML形式データ | 7swo_validation.xml.gz | 30.3 KB | 表示 | |
CIF形式データ | 7swo_validation.cif.gz | 44.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/sw/7swo ftp://data.pdbj.org/pub/pdb/validation_reports/sw/7swo | HTTPS FTP |
-関連構造データ
関連構造データ | 25477MC 7swnC 7swpC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 21901.570 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス) 遺伝子: S, 2 / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2 |
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#2: 抗体 | 分子量: 23368.225 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) |
#3: 抗体 | 分子量: 23214.668 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): expi293F / 発現宿主: Homo sapiens (ヒト) |
-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 |
-試料調製
構成要素 | 名称: C98C7 Fab in complex with WT SARS-CoV-2 RBD / タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES |
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分子量 | 実験値: NO |
緩衝液 | pH: 7.5 |
試料 | 濃度: 0.7 mg/ml / 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 |
-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: 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 |
撮影 | 電子線照射量: 52.208 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
EMソフトウェア | 名称: RELION / バージョン: 3.1 / カテゴリ: 3次元再構成 |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3次元再構成 | 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 460948 / 対称性のタイプ: POINT |