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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7y6d | ||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD | ||||||
![]() | Spike glycoprotein | ||||||
![]() | VIRAL PROTEIN / trimer | ||||||
機能・相同性 | ![]() 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 | ![]() ![]() | ||||||
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: 4.39 Å | ||||||
![]() | Xu, J. / Song, Y. / Li, S. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. 著者: Yutong Song / Hangping Yao / Nanping Wu / Jialu Xu / Zheyuan Zhang / Cheng Peng / Shibo Li / Weizheng Kong / Yong Chen / Miaojin Zhu / Jiaqi Wang / Danrong Shi / Chongchong Zhao / Xiangyun Lu ...著者: Yutong Song / Hangping Yao / Nanping Wu / Jialu Xu / Zheyuan Zhang / Cheng Peng / Shibo Li / Weizheng Kong / Yong Chen / Miaojin Zhu / Jiaqi Wang / Danrong Shi / Chongchong Zhao / Xiangyun Lu / Martín Echavarría Galindo / Sai Li / ![]() 要旨: Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis ...Among the current five Variants of Concern, infections caused by SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, the architecture of intact Delta virions remains veiled. Moreover, pieces of molecular evidence for the detailed mechanism of S-mediated membrane fusion are missing. Here, we showed the pleomorphic nature of Delta virions from electron beam inactivated samples and reported the in situ structure and distribution of S on the authentic Delta variant. We also captured the virus-virus fusion events, which provided pieces of structural evidence for Delta's attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Besides, site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S than that of the WT S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 555.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 452.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 2.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 2.2 MB | 表示 | |
XML形式データ | ![]() | 89.4 KB | 表示 | |
CIF形式データ | ![]() | 135.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 141484.719 Da / 分子数: 3 / 由来タイプ: 天然 詳細: T19R, G142D, L452R, T478K, D614G, P681R, D950N are Variants observed in Delta. 由来: (天然) ![]() ![]() Variant: Delta variant / 参照: UniProt: P0DTC2 #2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: 糖 | ChemComp-NAG / 研究の焦点であるリガンドがあるか | N | |
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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 |
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試料調製
構成要素 | 名称: Severe acute respiratory syndrome coronavirus 2 / タイプ: VIRUS / Entity ID: #1 / 由来: NATURAL | |||||||||||||||||||||||||
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分子量 | 実験値: NO | |||||||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() | |||||||||||||||||||||||||
ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: YES / 単離: STRAIN / タイプ: VIRION | |||||||||||||||||||||||||
天然宿主 | 生物種: Homo sapiens | |||||||||||||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
急速凍結 | 装置: GATAN CRYOPLUNGE 3 / 凍結剤: NITROGEN |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 25851 |
画像スキャン | 横: 5760 / 縦: 4092 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: CTFs are applied to the projections of the map during 3D classification and 3D refinement. タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 674792 詳細: Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to ...詳細: Initial micrographs were deconvolved using Warp, and 7,950 spikes were manually picked from 474 micrographs for training Topaz neural network. The trained Topaz neural network was used to automatically pick the spikes. 674,792 particles were auto-picked by Topaz. | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C3 (3回回転対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.39 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 45252 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 118.79 / 空間: REAL | ||||||||||||||||||||||||||||||||
原子モデル構築 |
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