+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-18639 | |||||||||
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タイトル | Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2) | |||||||||
マップデータ | Sharpened refined map of BA-2.86 spike with ACE2. | |||||||||
試料 |
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キーワード | Viral protein / immune system / SARS-CoV-2 / ACE2 / RBD / Spike / glycoprotein / BA.2.86 / angiotensin converting enzyme 2 / receptor / coronavirus-2 | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; 金属プロテアーゼ / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / 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 / Potential therapeutics for SARS / 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 / symbiont entry into host cell / membrane raft / apical plasma membrane / 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 / virion membrane / cell surface / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Severe acute respiratory syndrome coronavirus 2 (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: 3.7 Å | |||||||||
データ登録者 | Ren J / Stuart DI / Duyvesteyn HME | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Cell Rep Med / 年: 2024 タイトル: A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. 著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / ...著者: Chang Liu / Daming Zhou / Aiste Dijokaite-Guraliuc / Piyada Supasa / Helen M E Duyvesteyn / Helen M Ginn / Muneeswaran Selvaraj / Alexander J Mentzer / Raksha Das / Thushan I de Silva / Thomas G Ritter / Megan Plowright / Thomas A H Newman / Lizzie Stafford / Barbara Kronsteiner / Nigel Temperton / Yuan Lui / Martin Fellermeyer / Philip Goulder / Paul Klenerman / Susanna J Dunachie / Michael I Barton / Mikhail A Kutuzov / Omer Dushek / / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton / 要旨: BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible ...BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility. #1: ジャーナル: Acta Crystallogr., Sect. D: Biol. Crystallogr. 年: 2019 タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix 著者: Liebschner D / Afonine PV #2: ジャーナル: Nature Methods / 年: 2017 タイトル: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination 著者: Punjani A / Rubinstein JL | |||||||||
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_18639.map.gz | 79.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-18639-v30.xml emd-18639.xml | 24 KB 24 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_18639.png | 56.8 KB | ||
Filedesc metadata | emd-18639.cif.gz | 7.4 KB | ||
その他 | emd_18639_half_map_1.map.gz emd_18639_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-18639 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18639 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_18639_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_18639_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_18639_validation.xml.gz | 12.9 KB | 表示 | |
CIF形式データ | emd_18639_validation.cif.gz | 15.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18639 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18639 | HTTPS FTP |
-関連構造データ
-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_18639.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Sharpened refined map of BA-2.86 spike with ACE2. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.46 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
-ハーフマップ: Half map A of BA-2.86 spike with ACE2.
ファイル | emd_18639_half_map_1.map | ||||||||||||
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注釈 | Half map A of BA-2.86 spike with ACE2. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map B of BA-2.86 spike with ACE2.
ファイル | emd_18639_half_map_2.map | ||||||||||||
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注釈 | Half map B of BA-2.86 spike with ACE2. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin co...
全体 | 名称: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin converting enzyme 2 (ACE2) |
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要素 |
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-超分子 #1: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin co...
超分子 | 名称: BA-2.86 variant SARS-CoV2 S protein complexed with angiotensin converting enzyme 2 (ACE2) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 詳細: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 variant of SARS-CoV2. Angiotensin converting enzyme 2 (ACE2) recombinantely expressed. |
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-超分子 #2: Angiotensin converting enzyme 2 (ACE2)
超分子 | 名称: Angiotensin converting enzyme 2 (ACE2) / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #2 詳細: Human Angiotensin converting enzyme 2 (hACE2) recombinantely expressed |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #3: BA-2.86 variant SARS-CoV2 S protein
超分子 | 名称: BA-2.86 variant SARS-CoV2 S protein / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #1 詳細: Spike protein recombinantly expressed using sequence of human-derived BA-2.86 variant of SARS-CoV2. |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
-分子 #1: Spike protein S2'
分子 | 名称: Spike protein S2' / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
分子量 | 理論値: 22.159053 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: VTNLCPFHEV FNATRFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKHSGNYD YWYRLFRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L QSYGFRPT ...文字列: VTNLCPFHEV FNATRFASVY AWNRTRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IKGNEVSQIA PGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKHSGNYD YWYRLFRKSK LKPFERDIST EIYQAGNKPC KGKGPNCYFP L QSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGP UniProtKB: Spike glycoprotein |
-分子 #2: Processed angiotensin-converting enzyme 2
分子 | 名称: Processed angiotensin-converting enzyme 2 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 69.982562 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...文字列: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYADHHHHHH UniProtKB: Angiotensin-converting enzyme 2 |
-分子 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 3 / コピー数: 6 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE |
詳細 | BA-2.86 Spike with angiotensin converting enzyme 2 (ACE2) at a 6-fold excess of S protein. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: TFS Selectris X / エネルギーフィルター - スリット幅: 10 eV |
撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 1 / 実像数: 9818 / 平均電子線量: 50.0 e/Å2 / 詳細: Images were collected in EER format. |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.6 µm / 最小 デフォーカス(公称値): 0.8 µm / 倍率(公称値): 165000 |
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 |
+画像解析
-原子モデル構築 1
初期モデル |
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詳細 | Phenix real space refinement with manual checks using coot. | ||||||||
精密化 | 空間: REAL / プロトコル: OTHER | ||||||||
得られたモデル | PDB-8qsq: |