+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-42531 | |||||||||
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タイトル | CryoEM structure of A/Perth/16/2009 H3 in complex with polyclonal Fab from mice immunized with H3 stem nanoparticles-15 days post immunization | |||||||||
マップデータ | Perth09H3 H3D15pFab_sharp | |||||||||
試料 |
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キーワード | cryoEMPEM / Flu Hemagglutinin / Central stem epitope / VH1-18 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
機能・相同性 | 機能・相同性情報 viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane 類似検索 - 分子機能 | |||||||||
生物種 | Influenza A virus (A型インフルエンザウイルス) / Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||
データ登録者 | Huang J / Han J / Ward AB | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Immunity / 年: 2024 タイトル: Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. 著者: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca ...著者: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca L Ursin / Mya Vu / Kathrin H Kirsch / Thavaleak Prum / Victoria C Rosado / Thalia Bracamonte-Moreno / Vintus Okonkwo / Julia Bals / Caitlin McCarthy / Usha Nair / Masaru Kanekiyo / Andrew B Ward / Aaron G Schmidt / Facundo D Batista / Daniel Lingwood / 要旨: Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, ...Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway. | |||||||||
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_42531.map.gz | 307.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-42531-v30.xml emd-42531.xml | 20 KB 20 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_42531_fsc.xml | 14.5 KB | 表示 | FSCデータファイル |
画像 | emd_42531.png | 86.1 KB | ||
Filedesc metadata | emd-42531.cif.gz | 6.4 KB | ||
その他 | emd_42531_half_map_1.map.gz emd_42531_half_map_2.map.gz | 300.5 MB 300.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-42531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42531 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_42531_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_42531_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_42531_validation.xml.gz | 23.9 KB | 表示 | |
CIF形式データ | emd_42531_validation.cif.gz | 30.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42531 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42531 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ut6MC 8ut3C 8ut4C 8ut5C 8ut7C 8ut8C 8ut9C 8uwaC M: このマップから作成された原子モデル 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
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_42531.map.gz / 形式: CCP4 / 大きさ: 325 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Perth09H3 H3D15pFab_sharp | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.725 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: Perth09H3 H3D15pFab halfA
ファイル | emd_42531_half_map_1.map | ||||||||||||
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注釈 | Perth09H3 H3D15pFab_halfA | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Perth09H3 H3D15pFab halfB
ファイル | emd_42531_half_map_2.map | ||||||||||||
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注釈 | Perth09H3 H3D15pFab_halfB | ||||||||||||
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 : Mice polyclonal Fab complex with one protomer of a H3 trimer
全体 | 名称: Mice polyclonal Fab complex with one protomer of a H3 trimer |
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要素 |
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-超分子 #1: Mice polyclonal Fab complex with one protomer of a H3 trimer
超分子 | 名称: Mice polyclonal Fab complex with one protomer of a H3 trimer タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3 |
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由来(天然) | 生物種: Influenza A virus (A型インフルエンザウイルス) |
-超分子 #2: Polyclonal Fab purified from mice sera
超分子 | 名称: Polyclonal Fab purified from mice sera / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1-#2 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: H3D15 pFab HC Fv_polyA
分子 | 名称: H3D15 pFab HC Fv_polyA / 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: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 10.741231 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-分子 #2: H3D15 pFab LC Fv_polyA
分子 | 名称: H3D15 pFab LC Fv_polyA / 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: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 9.124238 KDa |
配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-分子 #3: Hemagglutinin
分子 | 名称: Hemagglutinin / タイプ: protein_or_peptide / ID: 3 / 詳細: A/Perth/16/2009 H3 / コピー数: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Influenza A virus (A型インフルエンザウイルス) |
分子量 | 理論値: 62.701074 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQSSSTGE ICDSPHQILD GKNCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCFP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSKNSFFS RLNWLTHLNF K YPALNVTM ...文字列: QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQSSSTGE ICDSPHQILD GKNCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCFP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSKNSFFS RLNWLTHLNF K YPALNVTM PNNEQFDKLY IWGVHHPGTD KDQIFLYAQA SGRITVSTKR SQQTVSPNIG SRPRVRNIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC NSECITPNGS IPNDKPFQNV NRITYGACPR YVKQNTLKLA TGM RNVPEK QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFS EVEGR IQDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIGS IRNG TYDHDVYRDE ALNNRFQIKG GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH UniProtKB: Hemagglutinin |
-分子 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 5 / コピー数: 18 / 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
濃度 | 0.7 mg/mL | ||||||||
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緩衝液 | pH: 7.4 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | TFS GLACIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.5 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |