+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8dxt | ||||||
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タイトル | Fab arm of antibody GAR12 bound to the receptor binding domain of SARS-CoV-2. | ||||||
要素 |
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キーワード | ANTIVIRAL PROTEIN / anti-CoV-2 / antibodies / convalescent patients / receptor binding domain. | ||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 | Homo sapiens (ヒト) Severe acute respiratory syndrome coronavirus 2 (ウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.25 Å | ||||||
データ登録者 | Langley, D.B. / Christ, D. / Henry, J.Y. | ||||||
資金援助 | オーストラリア, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. 著者: Romain Rouet / Jake Y Henry / Matt D Johansen / Meghna Sobti / Harikrishnan Balachandran / David B Langley / Gregory J Walker / Helen Lenthall / Jennifer Jackson / Stephanie Ubiparipovic / ...著者: Romain Rouet / Jake Y Henry / Matt D Johansen / Meghna Sobti / Harikrishnan Balachandran / David B Langley / Gregory J Walker / Helen Lenthall / Jennifer Jackson / Stephanie Ubiparipovic / Ohan Mazigi / Peter Schofield / Deborah L Burnett / Simon H J Brown / Marianne Martinello / Bernard Hudson / Nicole Gilroy / Jeffrey J Post / Anthony Kelleher / Hans-Martin Jäck / Christopher C Goodnow / Stuart G Turville / William D Rawlinson / Rowena A Bull / Alastair G Stewart / Philip M Hansbro / Daniel Christ / 要旨: Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies ...Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design. | ||||||
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 | 8dxt.cif.gz | 263.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8dxt.ent.gz | 208.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8dxt.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 | 8dxt_validation.pdf.gz | 816.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8dxt_full_validation.pdf.gz | 826 KB | 表示 | |
XML形式データ | 8dxt_validation.xml.gz | 24.2 KB | 表示 | |
CIF形式データ | 8dxt_validation.cif.gz | 33.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dx/8dxt ftp://data.pdbj.org/pub/pdb/validation_reports/dx/8dxt | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: 抗体 | 分子量: 23351.973 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Light chain of Fab arm of antibody GAR12 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): ExpiCHO 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
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#2: 抗体 | 分子量: 24766.676 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Heavy chain of Fab arm of antibody GAR12, with a 6His tag at the C-terminus 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): ExpiCHO 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
#3: タンパク質 | 分子量: 22975.688 Da / 分子数: 1 / Fragment: receptor binding domain / 由来タイプ: 組換発現 詳細: SARS CoV-2 receptor binding domain residues 333-528 with a 6His tag at the C-terminus 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): ExpiCHO 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P0DTC2 |
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | N |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.51 Å3/Da / 溶媒含有率: 50.96 % / 解説: Rods |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5 詳細: An equal volume (2 uL) of protein solution at ~5 mg/mL (in 25 mM Tris (pH 8.0), 200 mM NaCl) was combined with well solution (100 mM ammonium citrate (pH 5.5), 20% (w/v) PEG3350. |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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放射光源 | 由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9537 Å | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年6月11日 | ||||||||||||||||||||||||||||||
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | ||||||||||||||||||||||||||||||
放射波長 | 波長: 0.9537 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 2.25→48.085 Å / Num. obs: 34125 / % possible obs: 100 % / 冗長度: 6.5 % / Biso Wilson estimate: 51.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 17.9 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-位相決定
位相決定 | 手法: 分子置換 | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB 5i1b (Fab) and generic SARS-CoV-2 RBD 解像度: 2.25→48.085 Å / SU ML: 0.35 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.51 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 154.09 Å2 / Biso mean: 71.7112 Å2 / Biso min: 29.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.25→48.085 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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精密化 TLS | 手法: refined / Origin x: -0.1506 Å / Origin y: -0.6405 Å / Origin z: -26.8762 Å
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精密化 TLSグループ |
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