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Yorodumi- EMDB-34259: cryo-EM structure of Omicron BA.5 S protein in complex with XGv282 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34259 | |||||||||
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Title | cryo-EM structure of Omicron BA.5 S protein in complex with XGv282 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / 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 / receptor-mediated endocytosis of virus by host cell / membrane fusion / 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: 3.2 Å | |||||||||
Authors | Xia XY / Zhang YY / Chi XM / Huang BD / Wu LS / Zhou Q | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Discov / Year: 2023 Title: Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants. Authors: Xiangyang Chi / Lingyun Xia / Guanying Zhang / Ximin Chi / Bangdong Huang / Yuanyuan Zhang / Zhengshan Chen / Jin Han / Liushu Wu / Zeya Li / Hancong Sun / Ping Huang / Changming Yu / Wei Chen / Qiang Zhou / Abstract: The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this ...The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this work, we carried out a systematic and comprehensive analysis of the reported spike protein antibodies, counting the epitopes and genotypes of these antibodies. We further comprehensively analyzed the impact of Omicron mutations on antibody epitopes and classified these antibodies according to their binding patterns. We found that the epitopes of the H-RBD class antibodies were significantly less affected by Omicron mutations than other classes. Binding and virus neutralization experiments showed that such antibodies could effectively inhibit the immune escape of Omicron. Cryo-EM results showed that this class of antibodies utilized a conserved mechanism to neutralize SARS-CoV-2. Our results greatly help us deeply understand the impact of Omicron mutations. Meanwhile, it also provides guidance and insights for developing Omicron antibodies and vaccines. #1: Journal: Signal Transduct Target Ther / Year: 2022 Title: Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination Authors: Chi XY | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34259.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-34259-v30.xml emd-34259.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_34259.png | 32 KB | ||
Others | emd_34259_half_map_1.map.gz emd_34259_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34259 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34259 | HTTPS FTP |
-Validation report
Summary document | emd_34259_validation.pdf.gz | 901.4 KB | Display | EMDB validaton report |
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Full document | emd_34259_full_validation.pdf.gz | 901 KB | Display | |
Data in XML | emd_34259_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_34259_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34259 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34259 | HTTPS FTP |
-Related structure data
Related structure data | 8gtoMC 8gtpC 8gtqC 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_34259.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: 1.077 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34259_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34259_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of Omicron BA.5 S protein in complex with XGv282
Entire | Name: Cryo-EM structure of Omicron BA.5 S protein in complex with XGv282 |
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Components |
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-Supramolecule #1: Cryo-EM structure of Omicron BA.5 S protein in complex with XGv282
Supramolecule | Name: Cryo-EM structure of Omicron BA.5 S protein in complex with XGv282 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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-Supramolecule #2: S protein of Omicron BA.5 variant
Supramolecule | Name: S protein of Omicron BA.5 variant / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: XGv282
Supramolecule | Name: XGv282 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 141.326812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLIT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS S ANNCTFEY ...String: MFVFLVLLPL VSSQCVNLIT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFCNDPFL DVYYHKNNKS WMESEFRVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLGRDLPQGF SALEPLVDLP IGINITRFQT LL ALHRSYL TPGDSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQP TESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVI RGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVGG NYNYRYRLFR KSNLKPFERD ISTEIYQAGN KPCNG VAGV NCYFPLQSYG FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTESN KKFLPF QQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSHRRA RSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNF SQILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQDV VNHNAQALNT L VKQLSSKF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE QYIKWPWYIW LGFIAGLIAI VMVTIMLCCM TSCCSCLKGC CSCGSCCKFD EDDSEPVLKG VKLHYT UniProtKB: Spike glycoprotein |
-Macromolecule #2: heavy chain of XGv282
Macromolecule | Name: heavy chain of XGv282 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.927359 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QLVQSGAEVK KPGSSVKVSC KASGDTFSSY TFSWVRQAPG QGLEWMGRSI PIVGKAIYAQ EFQGRVTISA DRSTTTVYME LSSLRSDDT AVYYCARDQS GFDFFYYDHW GQGTLVAV |
-Macromolecule #3: light chain of XGv282
Macromolecule | Name: light chain of XGv282 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.514561 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QSVLTQPPSA SGTPGQRVTI SCSGSGSNIG SNTINWYQQL PGTAPKVLIY RNNERPSGVP DRFSGSKSGT SASLTISGLQ SEDEAYYHC AAWDDSLNGP VFGGGTKLTV LG |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 33 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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: GATAN K3 BIOQUANTUM (6k 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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 350760 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |