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Yorodumi- EMDB-36648: Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36648 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) | |||||||||
Map data | Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) | |||||||||
Sample |
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Keywords | Complex / SARS-CoV-1 / antibody / Homo sapiens / RBD / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.94 Å | |||||||||
Authors | Zhu JY | |||||||||
Funding support | China, 2 items
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Citation | Journal: Immunity / Year: 2023 Title: Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Authors: Ruoke Wang / Yang Han / Rui Zhang / Jiayi Zhu / Xuanyu Nan / Yaping Liu / Ziqing Yang / Bini Zhou / Jinfang Yu / Zichun Lin / Jinqian Li / Peng Chen / Yangjunqi Wang / Yujie Li / Dongsheng ...Authors: Ruoke Wang / Yang Han / Rui Zhang / Jiayi Zhu / Xuanyu Nan / Yaping Liu / Ziqing Yang / Bini Zhou / Jinfang Yu / Zichun Lin / Jinqian Li / Peng Chen / Yangjunqi Wang / Yujie Li / Dongsheng Liu / Xuanling Shi / Xinquan Wang / Qi Zhang / Yuhe R Yang / Taisheng Li / Linqi Zhang / Abstract: The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to ...The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36648.map.gz | 306.6 MB | EMDB map data format | |
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Header (meta data) | emd-36648-v30.xml emd-36648.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_36648.png | 66.8 KB | ||
Filedesc metadata | emd-36648.cif.gz | 4.3 KB | ||
Others | emd_36648_half_map_1.map.gz emd_36648_half_map_2.map.gz | 301.9 MB 301.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36648 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36648 | HTTPS FTP |
-Validation report
Summary document | emd_36648_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_36648_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_36648_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_36648_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36648 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36648 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36648.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of SARS-CoV-1 2P spike protein protomer...
File | emd_36648_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of SARS-CoV-1 2P spike protein protomer...
File | emd_36648_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-1 2P spike protein in complex with W328-6E10
Entire | Name: SARS-CoV-1 2P spike protein in complex with W328-6E10 |
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Components |
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-Supramolecule #1: SARS-CoV-1 2P spike protein in complex with W328-6E10
Supramolecule | Name: SARS-CoV-1 2P spike protein in complex with W328-6E10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4 Details: Cryo-EM structure of SARS-CoV-1 2P spike protein protomer in complex with W328-6E10 (local refine) |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus |
-Supramolecule #2: Severe acute respiratory syndrome coronavirus-1 2P
Supramolecule | Name: Severe acute respiratory syndrome coronavirus-1 2P / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3 / Details: SARS-CoV-1 2P |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus |
-Supramolecule #3: W328-6E10
Supramolecule | Name: W328-6E10 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 / Details: W328-6E10 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 6009 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |