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Yorodumi- EMDB-37157: State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37157 | |||||||||
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Title | State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||
Authors | Sun L / Mao Q / Wang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2024 Title: Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination. Authors: Xiaoyu Zhao / Tianyi Qiu / Xiner Huang / Qiyu Mao / Yajie Wang / Rui Qiao / Jiayan Li / Tiantian Mao / Yuan Wang / Yewei Cun / Caicui Wang / Cuiting Luo / Chaemin Yoon / Xun Wang / Chen Li / ...Authors: Xiaoyu Zhao / Tianyi Qiu / Xiner Huang / Qiyu Mao / Yajie Wang / Rui Qiao / Jiayan Li / Tiantian Mao / Yuan Wang / Yewei Cun / Caicui Wang / Cuiting Luo / Chaemin Yoon / Xun Wang / Chen Li / Yuchen Cui / Chaoyue Zhao / Minghui Li / Yanjia Chen / Guonan Cai / Wenye Geng / Zixin Hu / Jinglei Cao / Wenhong Zhang / Zhiwei Cao / Hin Chu / Lei Sun / Pengfei Wang / Abstract: The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the ...The current SARS-CoV-2 variants strikingly evade all authorized monoclonal antibodies and threaten the efficacy of serum-neutralizing activity elicited by vaccination or prior infection, urging the need to develop antivirals against SARS-CoV-2 and related sarbecoviruses. Here, we identified both potent and broadly neutralizing antibodies from a five-dose vaccinated donor who exhibited cross-reactive serum-neutralizing activity against diverse coronaviruses. Through single B-cell sorting and sequencing followed by a tailor-made computational pipeline, we successfully selected 86 antibodies with potential cross-neutralizing ability from 684 antibody sequences. Among them, PW5-570 potently neutralized all SARS-CoV-2 variants that arose prior to Omicron BA.5, and the other three could broadly neutralize all current SARS-CoV-2 variants of concern, SARS-CoV and their related sarbecoviruses (Pangolin-GD, RaTG13, WIV-1, and SHC014). Cryo-EM analysis demonstrates that these antibodies have diverse neutralization mechanisms, such as disassembling spike trimers, or binding to RBM or SD1 to affect ACE2 binding. In addition, prophylactic administration of these antibodies significantly protects nasal turbinate and lung infections against BA.1, XBB.1, and SARS-CoV viral challenge in golden Syrian hamsters, respectively. Importantly, post-exposure treatment with PW5-5 and PW5-535 also markedly protects against XBB.1 challenge in these models. This study reveals the potential utility of computational process to assist screening cross-reactive antibodies, as well as the potency of vaccine-induced broadly neutralizing antibodies against current SARS-CoV-2 variants and related sarbecoviruses, offering promising avenues for the development of broad therapeutic antibody drugs. | |||||||||
History |
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-Structure visualization
-Downloads & links
-EMDB archive
Map data | emd_37157.map.gz | 62.6 MB | EMDB map data format | |
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Header (meta data) | emd-37157-v30.xml emd-37157.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_37157.png | 140.8 KB | ||
Filedesc metadata | emd-37157.cif.gz | 6.8 KB | ||
Others | emd_37157_half_map_1.map.gz emd_37157_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37157 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37157 | HTTPS FTP |
-Validation report
Summary document | emd_37157_validation.pdf.gz | 895.7 KB | Display | EMDB validaton report |
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Full document | emd_37157_full_validation.pdf.gz | 895.3 KB | Display | |
Data in XML | emd_37157_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_37157_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37157 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37157 | HTTPS FTP |
-Related structure data
Related structure data | 8kehMC 8kdmC 8kdrC 8kdsC 8kdtC 8kejC 8kekC 8keoC 8kepC 8keqC 8kerC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37157.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS spike protein (S) in complex with broadly neutralizing antib...
Entire | Name: SARS spike protein (S) in complex with broadly neutralizing antibody PW5-5 |
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Components |
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-Supramolecule #1: SARS spike protein (S) in complex with broadly neutralizing antib...
Supramolecule | Name: SARS spike protein (S) in complex with broadly neutralizing antibody PW5-5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Details: XBB spike / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 143.147531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS ...String: MPMGSLQPLA TLYLLGMLVA SVLAQCVNLI TRTQSYTNSF TRGVYYPDKV FRSSVLHSTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDN PVLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYQKNNKSW M ESEFRVYS SANNCTFEYV SQPFLMDLEG KEGNFKNLRE FVFKNIDGYF KIYSKHTPIN LERDLPQGFS ALEPLVDLPI GI NITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIY QTSNFR VQPTESIVRF PNITNLCPFH EVFNATTFAS VYAWNRKRIS NCVADYSVIY NFAPFFAFKC YGVSPTKLND LCFT NVYAD SFVIRGNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKPSGN YNYLYRLFRK SKLKPFERDI STEIY QAGN KPCNGVAGSN CYSPLQSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLT ESN KKFLPFQQFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTW RV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIA I PTNFTISVTT EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPP IKYFGGFNFS QILPDPSKPS KRSPIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTI TSGWTFGAGP ALQIPFPMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTP SALGKLQDVV N HNAQALNT LVKQLSSKFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CV LGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQ IITTDN TFVSGNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNL NESLI DLQELGKYEQ GSGYIPEAPR DGQAYVRKDG EWVFLSTFLS GLEVLFQGPG GWSHPQFEKG GGSGGGSGGS AWSHP QFEK GGSHHHHHHH H UniProtKB: Spike glycoprotein |
-Macromolecule #2: PW5-5 light chain
Macromolecule | Name: PW5-5 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.782463 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ATNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ HRSNWPRMFT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ATNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ HRSNWPRMFT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC |
-Macromolecule #3: PW5-5 heavy chain
Macromolecule | Name: PW5-5 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.374523 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGASVKV SCKTSGYTFT DHYMYWVRQA PGQGLEWMGV INPDAGSVTY AQKFQGRVTM TSDTSTSTVY MELSSLRSE DTAVYYCARD LFFIPAANSF DYWGQGTLVT VSSTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String: QVQLVQSGAE VKKPGASVKV SCKTSGYTFT DHYMYWVRQA PGQGLEWMGV INPDAGSVTY AQKFQGRVTM TSDTSTSTVY MELSSLRSE DTAVYYCARD LFFIPAANSF DYWGQGTLVT VSSTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT CPPCPAPELL GG PSVFLFP PKPKDTLMIS RTPEVTCVVV DVSHEDPEVK FNWYVDGVEV HNAKTKPREE QYNSTYRVVS VLTVLHQDWL NGK EYKCKV SNKALPAPIE KTISKAKGQP REPQVYTLPP SRDELTKNQV SLTCLVKGFY PSDIAVEWES NGQPENNYKT TPPV LDSDG SFFLYSKLTV DKSRWQQGNV FSCSVLHEAL HSHYTQKSLS LSPGK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130701 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |