+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6zp5 | ||||||||||||||||||
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タイトル | SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation) | ||||||||||||||||||
要素 | Spike glycoprotein | ||||||||||||||||||
キーワード | VIRAL PROTEIN / Spike / Prefusion / Flexibility / Closed | ||||||||||||||||||
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 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) | ||||||||||||||||||
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: 3.1 Å | ||||||||||||||||||
データ登録者 | Martinez, M. / Marabini, R. / Carazo, J.M. | ||||||||||||||||||
資金援助 | スペイン, 米国, 5件
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引用 | ジャーナル: IUCrJ / 年: 2020 タイトル: Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. 著者: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del ...著者: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del Caño / Patricia Losana / Yunior C Fonseca-Reyna / Pablo Conesa / Daniel Wrapp / Pablo Chacon / Jason S McLellan / Hemant D Tagare / Jose-Maria Carazo / 要旨: Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been ...Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results. #1: ジャーナル: bioRxiv / 年: 2020 タイトル: Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures. 著者: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del ...著者: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del Caño / Patricia Losana / Yunior C Fonseca-Reyna / Pablo Conesa / Daniel Wrapp / Pablo Chacon / Jason S McLellan / Hemant D Tagare / Jose-Maria Carazo / 要旨: With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We ...With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results. | ||||||||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6zp5.cif.gz | 542.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6zp5.ent.gz | 415.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6zp5.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 | 6zp5_validation.pdf.gz | 2.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6zp5_full_validation.pdf.gz | 2.7 MB | 表示 | |
XML形式データ | 6zp5_validation.xml.gz | 89.9 KB | 表示 | |
CIF形式データ | 6zp5_validation.cif.gz | 139.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zp5 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zp5 | HTTPS FTP |
-関連構造データ
関連構造データ | 11336MC 6zowC 6zp7C C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10516 (タイトル: Cryo electron microscopy of SARS-CoV-2 spike in prefusion state Data size: 2.1 TB / Data #1: 2.outputMovies [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 / 非ポリマー , 2種, 6分子 ABC
#1: タンパク質 | 分子量: 142399.375 Da / 分子数: 3 / 変異: K986P, V987P / 由来タイプ: 組換発現 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス) 遺伝子: S, 2 / プラスミド: palphaH / 細胞株 (発現宿主): FreeStyle293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2 #8: 化合物 | |
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-糖 , 6種, 47分子
#2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: 多糖 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: 糖 | ChemComp-NAG / #7: 糖 | |
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-詳細
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 |
-試料調製
構成要素 | 名称: SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation) タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) / 細胞: FreeStyle293F / プラスミド: palphaH |
緩衝液 | pH: 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 36 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 45000 / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT 詳細: Atomic structure 6ZOW was flexibly fitted to the map. | ||||||||||||||||
原子モデル構築 | PDB-ID: 6ZOW |