+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7e7d | ||||||
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タイトル | Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate | ||||||
要素 | Spike glycoprotein,Collagen alpha-1(I) chain | ||||||
キーワード | VIRAL PROTEIN / spike protein / COVID-19 / vaccine | ||||||
機能・相同性 | 機能・相同性情報 cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Defective VWF binding to collagen type I ...cellular response to fluoride / collagen type I trimer / tooth mineralization / cellular response to vitamin E / collagen type IV trimer / Anchoring fibril formation / Crosslinking of collagen fibrils / collagen biosynthetic process / Collagen chain trimerization / Defective VWF binding to collagen type I / platelet-derived growth factor binding / bone trabecula formation / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / intramembranous ossification / embryonic skeletal system development / Extracellular matrix organization / extracellular matrix structural constituent conferring tensile strength / cartilage development involved in endochondral bone morphogenesis / Collagen biosynthesis and modifying enzymes / skin morphogenesis / collagen-activated tyrosine kinase receptor signaling pathway / endochondral ossification / Platelet Adhesion to exposed collagen / cellular response to fibroblast growth factor stimulus / collagen fibril organization / negative regulation of cell-substrate adhesion / response to steroid hormone / face morphogenesis / Scavenging by Class A Receptors / skin development / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / GP1b-IX-V activation signalling / blood vessel development / RUNX2 regulates osteoblast differentiation / Platelet Aggregation (Plug Formation) / Collagen degradation / protein localization to nucleus / Non-integrin membrane-ECM interactions / ECM proteoglycans / response to hyperoxia / Integrin cell surface interactions / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / cellular response to retinoic acid / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / cellular response to transforming growth factor beta stimulus / response to cAMP / visual perception / ossification / extracellular matrix organization / secretory granule / skeletal system development / cellular response to glucose stimulus / Cell surface interactions at the vascular wall / sensory perception of sound / cellular response to amino acid stimulus / response to insulin / response to hydrogen peroxide / osteoblast differentiation / cellular response to mechanical stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein transport / positive regulation of canonical Wnt signaling pathway / response to estradiol / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / Maturation of spike protein / viral translation / protease binding / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / 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 類似検索 - 分子機能 | ||||||
生物種 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) Homo sapiens (ヒト) | ||||||
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: 3.2 Å | ||||||
データ登録者 | Zheng, S. / Ma, J. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: J Virol / 年: 2021 タイトル: Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19. 著者: Jiahao Ma / Danmei Su / Yinyan Sun / Xueqin Huang / Ying Liang / Linqiang Fang / Yan Ma / Wenhui Li / Peng Liang / Sanduo Zheng / 要旨: Within a year after its emergence, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people worldwide with a death toll over 2 million. Vaccination ...Within a year after its emergence, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 100 million people worldwide with a death toll over 2 million. Vaccination remains the best hope to ultimately put this pandemic to an end. Here, using Trimer-Tag technology, we produced both wild-type (WT) and furin site mutant (MT) S-Trimers for COVID-19 vaccine studies. Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 Å and 2.6 Å respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. The tightly closed conformation is stabilized by fatty acid and polysorbate 80 binding at the receptor binding domains (RBDs) and the N terminal domains (NTDs) respectively. Additionally, we identified an important pH switch in the WT S-Trimer that shows dramatic conformational change and accounts for its increased stability at lower pH. These results validate Trimer-Tag as a platform technology in production of metastable WT S-Trimer as a candidate for COVID-19 subunit vaccine.Effective vaccine against SARS-CoV-2 is critical to end the COVID-19 pandemic. Here, using Trimer-Tag technology, we are able to produce stable and large quantities of WT S-Trimer, a subunit vaccine candidate for COVID-19 with high safety and efficacy from animal and Phase 1 clinical trial studies. Cryo-EM structures of the S-Trimer subunit vaccine candidate show that it predominately adopts tightly closed pre-fusion state, and resembles that of the native and full-length spike in detergent, confirming its structural integrity. WT S-Trimer is currently being evaluated in global Phase 2/3 clinical trial. Combining with published structures of the S protein, we also propose a model to dissect the conformation change of the spike protein before receptor binding. | ||||||
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 | 7e7d.cif.gz | 598.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7e7d.ent.gz | 491.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7e7d.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 | 7e7d_validation.pdf.gz | 2.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7e7d_full_validation.pdf.gz | 2.2 MB | 表示 | |
XML形式データ | 7e7d_validation.xml.gz | 86.5 KB | 表示 | |
CIF形式データ | 7e7d_validation.cif.gz | 135.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/e7/7e7d ftp://data.pdbj.org/pub/pdb/validation_reports/e7/7e7d | 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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-要素
#1: タンパク質 | 分子量: 168164.328 Da / 分子数: 3 / 由来タイプ: 組換発現 / 詳細: Chimeric protein 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス), (組換発現) Homo sapiens (ヒト) 遺伝子: S, 2, COL1A1 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 参照: UniProt: P0DTC2, UniProt: P02452 #2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: 糖 | ChemComp-NAG / #4: 化合物 | 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 protein fused to the C-terminal region of human type 1a collagen タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT | ||||||||||||
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分子量 | 実験値: NO | ||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: Cricetulus griseus (モンゴルキヌゲネズミ) | ||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: monodisperse | ||||||||||||
試料支持 | グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 282 K 詳細: blot time 2 seconds, blot force 4, waiting time 8 seconds |
-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: TFS 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 / 倍率(公称値): 64000 X / Calibrated defocus min: 600 nm / 最大 デフォーカス(補正後): 2800 nm / Cs: 0 mm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 50 e/Å2 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: 2 / 実像数: 2000 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.16_3549: / 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: 1504770 | ||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 173288 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6VXX | ||||||||||||||||||||||||||||||
精密化 | 最高解像度: 3.2 Å | ||||||||||||||||||||||||||||||
拘束条件 |
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