+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-34940 | |||||||||
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タイトル | Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 | |||||||||
マップデータ | Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 | |||||||||
試料 |
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キーワード | SARS-CoV-2 / Omicron BA.4 S-trimer / Cryo-EM structure / fab / IMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex | |||||||||
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) / Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.85 Å | |||||||||
データ登録者 | Gao GF / Liu S | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Cell Discov / 年: 2023 タイトル: Dosing interval regimen shapes potency and breadth of antibody repertoire after vaccination of SARS-CoV-2 RBD protein subunit vaccine. 著者: Shuxin Guo / Yuxuan Zheng / Zhengrong Gao / Minrun Duan / Sheng Liu / Pan Du / XiaoYu Xu / Kun Xu / Xin Zhao / Yan Chai / Peiyi Wang / Qi Zhao / George F Gao / Lianpan Dai / 要旨: Vaccination with different vaccines has been implemented globally to counter the continuous COVID-19 pandemic. However, the vaccine-elicited antibodies have reduced efficiency against the highly ...Vaccination with different vaccines has been implemented globally to counter the continuous COVID-19 pandemic. However, the vaccine-elicited antibodies have reduced efficiency against the highly mutated Omicron sub-variants. Previously, we developed a protein subunit COVID-19 vaccine called ZF2001, based on the dimeric receptor-binding domain (RBD). This vaccine has been administered using different dosing intervals in real-world setting. Some individuals received three doses of ZF2001, with a one-month interval between each dose, due to urgent clinical requirements. Others had an extended dosing interval of up to five months between the second and third dose, a standard vaccination regimen for the protein subunit vaccine against hepatitis B. In this study, we profile B cell responses in individuals who received three doses of ZF2001, and compared those with long or short dosing intervals. We observed that the long-interval group exhibited higher and broader serologic antibody responses. These responses were associated with the increased size and evolution of vaccine-elicited B-cell receptor repertoires, characterized by the elevation of expanded clonotypes and somatic hypermutations. Both groups of individuals generated substantial amounts of broadly neutralizing antibodies (bnAbs) against various SARS-CoV-2 variants, including Omicron sub-variants such as XBB. These bnAbs target four antigenic sites within the RBD. To determine the vulnerable site of SARS-CoV-2, we employed cryo-electron microscopy to identify the epitopes of highly potent bnAbs that targeted two major sites. Our findings provide immunological insights into the B cell responses elicited by RBD-based vaccine, and suggest that a vaccination regimen of prolonging time interval should be used in practice. | |||||||||
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_34940.map.gz | 483.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-34940-v30.xml emd-34940.xml | 19.9 KB 19.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_34940.png | 99.2 KB | ||
Filedesc metadata | emd-34940.cif.gz | 6.6 KB | ||
その他 | emd_34940_half_map_1.map.gz emd_34940_half_map_2.map.gz | 475.2 MB 475.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-34940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34940 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_34940_validation.pdf.gz | 775.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_34940_full_validation.pdf.gz | 775.4 KB | 表示 | |
XML形式データ | emd_34940_validation.xml.gz | 18.8 KB | 表示 | |
CIF形式データ | emd_34940_validation.cif.gz | 22.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34940 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34940 | 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_34940.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.84 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: Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in...
ファイル | emd_34940_half_map_1.map | ||||||||||||
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注釈 | Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in...
ファイル | emd_34940_half_map_2.map | ||||||||||||
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注釈 | Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 | ||||||||||||
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 : Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex ...
全体 | 名称: Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 |
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要素 |
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-超分子 #1: Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex ...
超分子 | 名称: Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#5 |
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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: 3 / 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) 株: Omicron/BA.4 |
分子量 | 理論値: 125.33618 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF ...文字列: QCVNLITRTQ SYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AISGTNGTKR FDNPVLPFND GVYFASTEKS NIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT FEYVSQPFLM D LEGKQGNF KNLREFVFKN IDGYFKIYSK HTPINLVRDL PQGFSALEPL VDLPIGINIT RFQTLLALHR SYLTPGDSSS GW TAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPF DEVFNA TRFASVYAWN RKRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIRG NEVSQIAPGQ TGNI ADYNY KLPDDFTGCV IAWNSNKLDS KVGGNYNYRY RLFRKSNLKP FERDISTEIY QAGNKPCNGV AGVNCYFPLQ SYGFR PTYG VGHQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVNFN FNGLTGTGVL TESNKKFLPF QQFGRDIADT TDAVRD PQT LEILDITPCS FGGVSVITPG TNTSNQVAVL YQGVNCTEVP VAIHADQLTP TWRVYSTGSN VFQTRAGCLI GAEYVNN SY ECDIPIGAGI CASYQTQTNS PRRARSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDC T MYICGDSTEC SNLLLQYGSF CTQLKRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKYFGG FNFSQILPDP SKPSKRSPI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGPALQIPF PMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTPSALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSVL N DILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PH GVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVY DPLQPE LDS UniProtKB: Spike glycoprotein |
-分子 #2: fab L4.65
分子 | 名称: fab L4.65 / タイプ: protein_or_peptide / ID: 2 / コピー数: 3 / 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: 24.953938 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVAWIR QPPGKALEWL ALIYWDNDKR SSPSLNNRLT ITKDTSKNQV VLTMTNMDP EDTATYYCAH FFSHYDSSNY YYGSWFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...文字列: QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVAWIR QPPGKALEWL ALIYWDNDKR SSPSLNNRLT ITKDTSKNQV VLTMTNMDP EDTATYYCAH FFSHYDSSNY YYGSWFDPWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSC |
-分子 #3: fab L4.65
分子 | 名称: fab L4.65 / タイプ: protein_or_peptide / ID: 3 / コピー数: 3 / 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: 23.556061 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: EIVLTQSPGT LSLSPGERAT LSCRASQSFD SRYLGWYQQK SGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQFGDSPFTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...文字列: EIVLTQSPGT LSLSPGERAT LSCRASQSFD SRYLGWYQQK SGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQFGDSPFTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-分子 #4: fab L5.34
分子 | 名称: fab L5.34 / タイプ: protein_or_peptide / ID: 4 / コピー数: 3 / 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: 23.592424 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: VQLVESGGGL VQPGGSLRLS CAASEITVSS NYMNWVRQAP GKGLEWVSVV YPGGSTFYTD SVKGRFTISR DNSKNTLYLQ MNSLRAEDT AVYYCARESG GFPLAEGAFD IWGQGTMVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...文字列: VQLVESGGGL VQPGGSLRLS CAASEITVSS NYMNWVRQAP GKGLEWVSVV YPGGSTFYTD SVKGRFTISR DNSKNTLYLQ MNSLRAEDT AVYYCARESG GFPLAEGAFD IWGQGTMVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSC |
-分子 #5: fab L5.34
分子 | 名称: fab L5.34 / タイプ: protein_or_peptide / ID: 5 / コピー数: 3 / 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: 23.379928 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: DIQMTQSPSS LSASVGDRVS ITCRASQSIS THLHWYQQKP GKAPKLLISA ASTLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ QSYSTPRGLS FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...文字列: DIQMTQSPSS LSASVGDRVS ITCRASQSIS THLHWYQQKP GKAPKLLISA ASTLQSGVPS RFSGSGSGTD FTLTITSLQP EDFATYYCQ QSYSTPRGLS FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-分子 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 6 / コピー数: 3 / 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: 8 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: 1.39 e/Å2 |
電子線 | 加速電圧: 300 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): 5.0 µm / 最小 デフォーカス(公称値): 1.2 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.85 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 593563 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: OTHER |