+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8wzi | |||||||||
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タイトル | One RBD up state of Spike glycoprotein, SARS-CoV-2 | |||||||||
要素 | Spike glycoprotein | |||||||||
キーワード | VIRAL PROTEIN / Glycoprotein / SARS-CoV-2 | |||||||||
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 / 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 / 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 Å | |||||||||
データ登録者 | Yadav, S. / Vinothkumar, K.R. | |||||||||
資金援助 | インド, 2件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2024 タイトル: Factors affecting macromolecule orientations in thin films formed in cryo-EM. 著者: Swati Yadav / Kutti R Vinothkumar / 要旨: The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the ...The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour. | |||||||||
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 | 8wzi.cif.gz | 629.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8wzi.ent.gz | 507.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8wzi.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 | 8wzi_validation.pdf.gz | 2.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8wzi_full_validation.pdf.gz | 2.8 MB | 表示 | |
XML形式データ | 8wzi_validation.xml.gz | 92.3 KB | 表示 | |
CIF形式データ | 8wzi_validation.cif.gz | 141 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wz/8wzi ftp://data.pdbj.org/pub/pdb/validation_reports/wz/8wzi | HTTPS FTP |
-関連構造データ
関連構造データ | 37953MC 8wv4C 8wv5C 8wv6C 8wzhC 8wzjC 8wzkC 8wzmC 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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-要素
#1: タンパク質 | 分子量: 139706.984 Da / 分子数: 3 / 変異: (RRAR)682A,K986P, V987P / 由来タイプ: 組換発現 詳細: linker (1216-SGRLVPRGSP-1225) and a fibritin trimerization motif (1226-GSGYIPEAPRDGQAYVRKDGEWVLLSTFLG-1254) followed by another linker (1256-GTK-1258) followed by the HRV3c post cleavage ...詳細: linker (1216-SGRLVPRGSP-1225) and a fibritin trimerization motif (1226-GSGYIPEAPRDGQAYVRKDGEWVLLSTFLG-1254) followed by another linker (1256-GTK-1258) followed by the HRV3c post cleavage fragment (1259-LEVLFQ-1264) 由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス) 遺伝子: S / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2 #2: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | #4: 多糖 | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #5: 糖 | ChemComp-NAG / 研究の焦点であるリガンドがあるか | Y | |
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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: Spike glycoprotein, SARS-CoV-2 / タイプ: COMPLEX / Entity ID: #1 / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 値: 0.432 MDa / 実験値: NO | ||||||||||||||||||||
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) | ||||||||||||||||||||
緩衝液 | pH: 8 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 2 mg/ml / 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: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R0.6/1 | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 293 K / 詳細: Blot force, 0 |
-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 / 倍率(公称値): 75000 X / 倍率(補正後): 130841 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): 1800 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE |
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 | 平均露光時間: 60 sec. / 電子線照射量: 25 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 撮影したグリッド数: 1 / 詳細: Movies were collected at 40 frames per second |
画像スキャン | サンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 261703 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 84.6 / プロトコル: OTHER / 空間: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 8d56 Accession code: 8d56 / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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