+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31014 | |||||||||
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Title | SARS-CoV-2 S-6P in complex with 9 Fabs | |||||||||
Map data | ||||||||||
Sample |
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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: 3.16 Å | |||||||||
Authors | Du S / Xiao J / Zhang Z | |||||||||
Citation | Journal: Cell Res / Year: 2021 Title: Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li ...Authors: Yunlong Cao / Ayijiang Yisimayi / Yali Bai / Weijin Huang / Xiaofeng Li / Zhiying Zhang / Tianjiao Yuan / Ran An / Jing Wang / Tianhe Xiao / Shuo Du / Wenping Ma / Liyang Song / Yongzheng Li / Xiang Li / Weiliang Song / Jiajing Wu / Shuo Liu / Xuemei Li / Yonghong Zhang / Bin Su / Xianghua Guo / Yangyang Wei / Chuanping Gao / Nana Zhang / Yifei Zhang / Yang Dou / Xiaoyu Xu / Rui Shi / Bai Lu / Ronghua Jin / Yingmin Ma / Chengfeng Qin / Youchun Wang / Yingmei Feng / Junyu Xiao / Xiaoliang Sunney Xie / Abstract: SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 ...SARS-CoV-2 variants could induce immune escape by mutations on the receptor-binding domain (RBD) and N-terminal domain (NTD). Here we report the humoral immune response to circulating SARS-CoV-2 variants, such as 501Y.V2 (B.1.351), of the plasma and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine), ZF2001 (RBD-subunit vaccine) and natural infection. Among 86 potent NAbs identified by high-throughput single-cell VDJ sequencing of peripheral blood mononuclear cells from vaccinees and convalescents, near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination, with E484K being the dominant cause. VH3-53/VH3-66 recurrent antibodies respond differently to RBD variants, and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining regions. In contrast, the 242-244 deletion (242-244Δ) would abolish most neutralization activity of anti-NTD NAbs by interrupting the conformation of NTD antigenic supersite, indicating a much less diversity of anti-NTD NAbs than anti-RBD NAbs. Plasma of convalescents and CoronaVac vaccinees displayed comparable neutralization reductions against pseudo- and authentic 501Y.V2 variants, mainly caused by E484K/N501Y and 242-244Δ, with the effects being additive. Importantly, RBD-subunit vaccinees exhibit markedly higher tolerance to 501Y.V2 than convalescents, since the elicited anti-RBD NAbs display a high diversity and are unaffected by NTD mutations. Moreover, an extended gap between the third and second doses of ZF2001 leads to better neutralizing activity and tolerance to 501Y.V2 than the standard three-dose administration. Together, these results suggest that the deployment of RBD-vaccines, through a third-dose boost, may be ideal for combating SARS-CoV-2 variants when necessary, especially for those carrying mutations that disrupt the NTD supersite. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31014.map.gz | 21.2 MB | EMDB map data format | |
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Header (meta data) | emd-31014-v30.xml emd-31014.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_31014.png | 47.1 KB | ||
Masks | emd_31014_msk_1.map | 244.1 MB | Mask map | |
Others | emd_31014_half_map_1.map.gz emd_31014_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31014 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31014 | HTTPS FTP |
-Validation report
Summary document | emd_31014_validation.pdf.gz | 701.8 KB | Display | EMDB validaton report |
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Full document | emd_31014_full_validation.pdf.gz | 701.4 KB | Display | |
Data in XML | emd_31014_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_31014_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31014 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31014 | HTTPS FTP |
-Related structure data
Related structure data | 7e8cMC 7e7xC 7e7yC 7e86C 7e88C 7e8fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31014.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31014_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31014_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31014_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SARS-CoV-2 S-6P in complex with 9 Fabs
+Supramolecule #1: SARS-CoV-2 S-6P in complex with 9 Fabs
+Supramolecule #2: SARS-CoV-2 S
+Supramolecule #3: 604 H, 604 L, N9 H, 368-2 L, 368-2 H, N9 L
+Macromolecule #1: Spike glycoprotein
+Macromolecule #2: 604 H
+Macromolecule #3: 604 L
+Macromolecule #4: N9 H
+Macromolecule #5: 368-2 L
+Macromolecule #6: 368-2 H
+Macromolecule #7: N9 L
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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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 K2 QUANTUM (4k x 4k) / Average electron dose: 63.27 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178557 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |