+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23039 | |||||||||
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タイトル | Cryo-EM map of SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupted form) | |||||||||
マップデータ | SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupted form) | |||||||||
試料 |
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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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.78 Å | |||||||||
データ登録者 | Cerutti G / Shapiro L | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: bioRxiv / 年: 2021 タイトル: Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. 要旨: Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 ...Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2. HIGHLIGHTS: A molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralizationCryo-EM analyses detail the structure of a novel ...HIGHLIGHTS: A molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralizationCryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimerCryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spikeSequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chainsIGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires. | |||||||||
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_23039.map.gz | 229.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23039-v30.xml emd-23039.xml | 18 KB 18 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_23039.png | 133.9 KB | ||
その他 | emd_23039_additional_1.map.gz emd_23039_half_map_1.map.gz emd_23039_half_map_2.map.gz | 119.7 MB 226.8 MB 226.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23039 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23039_validation.pdf.gz | 998.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23039_full_validation.pdf.gz | 998.4 KB | 表示 | |
XML形式データ | emd_23039_validation.xml.gz | 15.8 KB | 表示 | |
CIF形式データ | emd_23039_validation.cif.gz | 18.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23039 | 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_23039.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupted form) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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
-追加マップ: Unsharpened map
ファイル | emd_23039_additional_1.map | ||||||||||||
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注釈 | Unsharpened map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half-volume 1
ファイル | emd_23039_half_map_1.map | ||||||||||||
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注釈 | half-volume 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: half-volume 2
ファイル | emd_23039_half_map_2.map | ||||||||||||
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注釈 | half-volume 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupt...
全体 | 名称: SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupted form) |
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要素 |
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-超分子 #1: SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupt...
超分子 | 名称: SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab (disrupted form) タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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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
緩衝液 | pH: 5.5 |
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凍結 | 凍結剤: ETHANE |
-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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 42.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: OTHER |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 5.78 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 188296 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |