+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7tpr | ||||||||||||||||||||||||
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タイトル | Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants | ||||||||||||||||||||||||
要素 |
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キーワード | VIRAL PROTEIN/IMMUNE SYSTEM / Neutralization / nanobody / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) Camelus dromedarius (ヒトコブラクダ) | ||||||||||||||||||||||||
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: 2.39 Å | ||||||||||||||||||||||||
データ登録者 | Butay, K.J. / Zhu, J. / Dandey, V.P. / Hong, J. / Kwon, H.J. / Chen, C.Z. / Duan, Z. / Li, D. / Ren, H. / Liang, T. ...Butay, K.J. / Zhu, J. / Dandey, V.P. / Hong, J. / Kwon, H.J. / Chen, C.Z. / Duan, Z. / Li, D. / Ren, H. / Liang, T. / Martin, N. / Esposito, D. / Ortega-Rodriguez, U. / Xu, M. / Xie, H. / Ho, M. / Cachau, R. / Borgnia, M.J. | ||||||||||||||||||||||||
資金援助 | 米国, 7件
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引用 | ジャーナル: bioRxiv / 年: 2021 タイトル: Camel nanobodies broadly neutralize SARS-CoV-2 variants. 著者: Jessica Hong / Hyung Joon Kwon / Raul Cachau / Catherine Z Chen / Kevin John Butay / Zhijian Duan / Dan Li / Hua Ren / Tianyuzhou Liang / Jianghai Zhu / Venkata P Dandey / Negin Martin / ...著者: Jessica Hong / Hyung Joon Kwon / Raul Cachau / Catherine Z Chen / Kevin John Butay / Zhijian Duan / Dan Li / Hua Ren / Tianyuzhou Liang / Jianghai Zhu / Venkata P Dandey / Negin Martin / Dominic Esposito / Uriel Ortega-Rodriguez / Miao Xu / Mario J Borgnia / Hang Xie / Mitchell Ho / 要旨: With the emergence of SARS-CoV-2 variants, there is urgent need to develop broadly neutralizing antibodies. Here, we isolate two V H nanobodies (7A3 and 8A2) from dromedary camels by phage display, ...With the emergence of SARS-CoV-2 variants, there is urgent need to develop broadly neutralizing antibodies. Here, we isolate two V H nanobodies (7A3 and 8A2) from dromedary camels by phage display, which have high affinity for the receptor-binding domain (RBD) and broad neutralization activities against SARS-CoV-2 and its emerging variants. Cryo-EM complex structures reveal that 8A2 binds the RBD in its up mode and 7A3 inhibits receptor binding by uniquely targeting a highly conserved and deeply buried site in the spike regardless of the RBD conformational state. 7A3 at a dose of ≥5 mg/kg efficiently protects K18-hACE2 transgenic mice from the lethal challenge of B.1.351 or B.1.617.2, suggesting that the nanobody has promising therapeutic potentials to curb the COVID-19 surge with emerging SARS-CoV-2 variants. ONE-SENTENCE SUMMARY: Dromedary camel ( ) V H phage libraries were built for isolation of the nanobodies that broadly neutralize SARS-CoV-2 variants. | ||||||||||||||||||||||||
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 | 7tpr.cif.gz | 693.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7tpr.ent.gz | 576.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7tpr.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 | 7tpr_validation.pdf.gz | 995.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7tpr_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 7tpr_validation.xml.gz | 110.4 KB | 表示 | |
CIF形式データ | 7tpr_validation.cif.gz | 165.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/tp/7tpr ftp://data.pdbj.org/pub/pdb/validation_reports/tp/7tpr | HTTPS FTP |
-関連構造データ
関連構造データ | 26062MC 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: 126821.453 Da / 分子数: 3 変異: F817P, A892P, A899P, A942P, K986P, V987P, and residues 682-685 from RRAR to GSAS 由来タイプ: 組換発現 / 詳細: Hexa-Pro construct mutations 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス) 遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2 #2: 抗体 | 分子量: 13993.344 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Camelus dromedarius (ヒトコブラクダ) 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): HB2151 #3: 抗体 | 分子量: 13755.188 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) Camelus dromedarius (ヒトコブラクダ) 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): HB2151 |
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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 |
-試料調製
構成要素 |
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分子量 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 / 詳細: PBS | ||||||||||||||||||||||||||||||
試料 | 濃度: 1.93 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: Complexes of spike with 7A3 and/or 8A2 VHHs were prepared by mixing the components at a spike trimer to nanobody molar ratio of 1:6. The final concentration of spike trimer was 3 uM in PBS at ...詳細: Complexes of spike with 7A3 and/or 8A2 VHHs were prepared by mixing the components at a spike trimer to nanobody molar ratio of 1:6. The final concentration of spike trimer was 3 uM in PBS at pH 7 with the addition of 5 mM imidazole. Because the 8A2 stock was too diluted, complexes involving this nanobody were prepared at 0.5 uM spike trimer followed by a 6-fold concentration using a 10 kDa cutoff centrifugal filter (Amicon Ultra). All complexes were incubated on ice for at least 5 min prior to grid preparation. | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Homemade | ||||||||||||||||||||||||||||||
急速凍結 | 装置: LEICA EM GP / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 298 K |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company / モデル: Titan Krios / 画像提供: FEI Company | |||||||||||||||||||||
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EM imaging | アライメント法: ZEMLIN TABLEAU / 電子線源: FIELD EMISSION GUN / 照射モード: FLOOD BEAM / モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2200 nm / 最小 デフォーカス(公称値): 1500 nm / 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1
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撮影 |
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画像スキャン | サンプリングサイズ: 5.000001 µm / 横: 5760 / 縦: 4092 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | ||||||||||||||||||||||||||||||
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EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1539054 | ||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.39 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 580888 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||
拘束条件 |
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