[English] 日本語
Yorodumi- EMDB-34410: SARS-CoV-2 BA.4 variants S ectodomain trimer in complex with neut... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34410 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 BA.4 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | SARS-CoV-2 BA.4 / antibody / VIRUS / 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 / Attachment and Entry / membrane fusion / 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: 2.9 Å | |||||||||
Authors | Wang X / Wang Z | |||||||||
Funding support | 1 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants. Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin ...Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin Tong / Xi Yu / Linjuan Wu / Dong Chen / Renli Zhang / Ningyi Jin / Weijun Shen / Jincun Zhao / Mingyao Tian / Xinquan Wang / Gong Cheng / Abstract: A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, ...A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, we offer insights into the inactivated vaccine-induced antibody responses after prime-boost vaccination at both the polyclonal and monoclonal levels. We characterized the VDJ sequence of 118 monoclonal antibodies (mAbs) and found that 20 neutralizing mAbs showed varied potency and breadth against a range of variants including XBB.1.5, BQ.1.1, and BN.1. Bispecific antibodies (bsAbs) based on nonoverlapping mAbs exhibited enhanced neutralizing potency and breadth against the most antibody-evasive strains, such as XBB.1.5, BQ.1.1, and BN.1. The passive transfer of mAbs or their bsAb effectively protected female hACE2 transgenic mice from challenge with an infectious Delta or Omicron BA.2 variant. The neutralization mechanisms of these antibodies were determined by structural characterization. Overall, a broad spectrum of potent and distinct neutralizing antibodies can be induced in individuals immunized with the SARS-CoV-2 inactivated vaccine BBIBP-CorV, suggesting the application potential of inactivated vaccines and these antibodies for preventing infection by SARS-CoV-2 circulating variants. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34410.map.gz | 141.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34410-v30.xml emd-34410.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_34410.png | 31.3 KB | ||
Others | emd_34410_half_map_1.map.gz emd_34410_half_map_2.map.gz | 139.1 MB 139.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34410 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34410 | HTTPS FTP |
-Validation report
Summary document | emd_34410_validation.pdf.gz | 814.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_34410_full_validation.pdf.gz | 813.9 KB | Display | |
Data in XML | emd_34410_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_34410_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34410 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34410 | HTTPS FTP |
-Related structure data
Related structure data | 8h07MC 7x2hC 7xd2C 8h08C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_34410.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_34410_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_34410_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV-2 BA.4 variants spike
Entire | Name: SARS-CoV-2 BA.4 variants spike |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 BA.4 variants spike
Supramolecule | Name: SARS-CoV-2 BA.4 variants spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
---|
-Supramolecule #2: SARS-CoV-2 BA.4 variants spike
Supramolecule | Name: SARS-CoV-2 BA.4 variants spike / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: antibody
Supramolecule | Name: antibody / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2-#5 |
---|---|
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 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 142.526797 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLG REPEDLPQGF 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 QTQTKSHGSA SSVASQSIIA 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 QGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWS HPQF EK |
-Macromolecule #2: 10-5B H chain
Macromolecule | Name: 10-5B H chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.517014 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LIQPGGSLRL SCAVSGFTVS RMSWVRQAPG KGLECVSVIY TGGNTDYADS VKGRFTISRD NSKNTLYLQM NSLRAEDTA LYYCVRGSGG IHDAFDIWGQ GTMVTVSS |
-Macromolecule #3: 10-5B L chain
Macromolecule | Name: 10-5B L chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.368661 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS VSASVGDRVT ITCRASQGIS TWLAWYQQKP GKAPKVLINA ASGLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QAHSFPPTFG PGTKLEIK |
-Macromolecule #4: 6-2C H chain
Macromolecule | Name: 6-2C H chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.723151 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVESGGG VVQPGRSLRL SCASSGFTFS TYHMHWVRQP PGKGLEWVAF ISYDGSNYYY SDSVKGRFTI SRDNSKNTVY LQMNSLRAE DTALYYCARD SSGWHWGVPF DYWGQGTLVT VSS |
-Macromolecule #5: 6-2C L chain
Macromolecule | Name: 6-2C L chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.685123 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPSS LSASVQDRVT ITCRASQVIS NYLAWFQQKP GKAPKLLIYA ASNLQSGVPS RFRGSGSGTD FTLTISSLQP EDFATYYCQ QYNIYPLTFG GGTKVDIK |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (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: 1.5 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: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 624379 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |