+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25686 | |||||||||
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タイトル | CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11 | |||||||||
マップデータ | Composite map obtained by combining focused, sharpened maps. Map used for model building and refinements. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 blood coagulation, common pathway / apicolateral plasma membrane / negative regulation of blood coagulation / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / response to X-ray / negative regulation of platelet activation / negative regulation of fibrinolysis / Common Pathway of Fibrin Clot Formation ...blood coagulation, common pathway / apicolateral plasma membrane / negative regulation of blood coagulation / serine-type endopeptidase complex / zymogen activation / vacuolar membrane / response to X-ray / negative regulation of platelet activation / negative regulation of fibrinolysis / Common Pathway of Fibrin Clot Formation / response to cAMP / female pregnancy / Cell surface interactions at the vascular wall / transmembrane signaling receptor activity / blood coagulation / signaling receptor activity / host cell endosome / host cell Golgi apparatus / response to lipopolysaccharide / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / viral envelope / calcium ion binding / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human betaherpesvirus 5 (ヘルペスウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Kschonsak M / Johnson MC / Schelling R / Green EM / Rouge L / Ho H / Patel N / Kilic C / Kraft E / Arthur CP ...Kschonsak M / Johnson MC / Schelling R / Green EM / Rouge L / Ho H / Patel N / Kilic C / Kraft E / Arthur CP / Rohou AL / Comps-Agrar L / Martinez-Martin N / Perez L / Payandeh J / Ciferri C | |||||||||
資金援助 | 1件
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引用 | ジャーナル: Sci Adv / 年: 2022 タイトル: Structural basis for HCMV Pentamer receptor recognition and antibody neutralization. 著者: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / Laetitia ...著者: Marc Kschonsak / Matthew C Johnson / Rachel Schelling / Evan M Green / Lionel Rougé / Hoangdung Ho / Nidhi Patel / Cem Kilic / Edward Kraft / Christopher P Arthur / Alexis L Rohou / Laetitia Comps-Agrar / Nadia Martinez-Martin / Laurent Perez / Jian Payandeh / Claudio Ciferri / 要旨: Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial ...Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_25686.map.gz | 13 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25686-v30.xml emd-25686.xml | 59.9 KB 59.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25686.png | 83.3 KB | ||
その他 | emd_25686_additional_1.map.gz emd_25686_additional_10.map.gz emd_25686_additional_11.map.gz emd_25686_additional_12.map.gz emd_25686_additional_13.map.gz emd_25686_additional_14.map.gz emd_25686_additional_15.map.gz emd_25686_additional_16.map.gz emd_25686_additional_2.map.gz emd_25686_additional_3.map.gz emd_25686_additional_4.map.gz emd_25686_additional_5.map.gz emd_25686_additional_6.map.gz emd_25686_additional_7.map.gz emd_25686_additional_8.map.gz emd_25686_additional_9.map.gz | 226.2 MB 165.7 MB 165.7 MB 8.2 MB 226.4 MB 165.7 MB 165.7 MB 12.3 MB 165.5 MB 13.7 MB 165.6 MB 226.3 MB 165.6 MB 165.7 MB 8.5 MB 226.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25686 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25686 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25686_validation.pdf.gz | 340.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25686_full_validation.pdf.gz | 339.8 KB | 表示 | |
XML形式データ | emd_25686_validation.xml.gz | 7 KB | 表示 | |
CIF形式データ | emd_25686_validation.cif.gz | 8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25686 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25686 | HTTPS FTP |
-関連構造データ
関連構造データ | 7t4rMC 7t4qC 7t4sC M: このマップから作成された原子モデル 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
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_25686.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 | Composite map obtained by combining focused, sharpened maps. Map used for model building and refinements. | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0726 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
+追加マップ: Non-sharpened, full map of overall map (not focused).
+追加マップ: Half map 1 of focused gH-gL (A) region.
+追加マップ: Half map 2 of focused gH-gL (A) region.
+追加マップ: Density modified map of focused gH-gL (A) map...
+追加マップ: Non-sharpened, full map of focused gH-gL (B) region.
+追加マップ: Half map 1 of focused gH-gL (B) region.
+追加マップ: Half map 2 of focused gH-gL (B) region.
+追加マップ: Density modified map of overall map (not focused)...
+追加マップ: Half map 1 of overall map (not focused).
+追加マップ: Density modified map of focused THBD-ULs map used...
+追加マップ: Half map 2 of overall map (not focused).
+追加マップ: Non-sharpened, full map of focused THBD-ULs region.
+追加マップ: Half map 1 of focused THBD-ULs region.
+追加マップ: Half map 2 of focused THBD-ULs region.
+追加マップ: Density modified map of focused gH-gL (B) map...
+追加マップ: Non-sharpened, full map of focused gH-gL (A) region.
-試料の構成要素
+全体 : Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to...
+超分子 #1: Complex of 2x HCMV Pentamer gH, gL, UL128, UL130, UL131A bound to...
+分子 #1: Thrombomodulin
+分子 #2: Envelope glycoprotein H
+分子 #3: Envelope glycoprotein L
+分子 #4: Envelope protein UL128
+分子 #5: Envelope glycoprotein UL130
+分子 #6: Envelope protein UL131A
+分子 #7: Fab 13H11 heavy chain
+分子 #8: Fab 13H11 light chain
+分子 #9: Fab MSL-109 light chain
+分子 #10: Fab MSL-109 heavy chain
+分子 #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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
濃度 | 0.6 mg/mL | |||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: UltrAuFoil R0.6/1 / 材質: GOLD / メッシュ: 300 詳細: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, ...詳細: The grid was incubated with a thiol reactive self-assembling reaction mixture of 4mM monothiolalkane(C11)PEG6-OH (11-mercaptoundecyl) hexaethyleneglycol, (SPT-0011P6, SensoPath Technologies, Inc., Bozeman, MT)[23]. Grids were incubated with this self-assembled, monolayer (SAM) solution for 24 hours. Prior to grid freezing, grids were removed from the SAM solution and rinsed with EtOH. | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: LEICA EM GP / 詳細: blot for 3.5s before plunging. |
-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) 撮影したグリッド数: 1 / 実像数: 10926 / 平均電子線量: 64.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |