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Yorodumi- EMDB-31822: Negative staining (NS)-EM structure of SARS-CoV-2 S-Kappa variant... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31822 | |||||||||||||||
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Title | Negative staining (NS)-EM structure of SARS-CoV-2 S-Kappa variant in complex with neutralizing antibody RBD-chAb-25 | |||||||||||||||
Map data | NSEM structure of SARS-CoV-2 S-Kappa variant in complex with neutralizing antibody RBD-chAb-25 | |||||||||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.0 Å | |||||||||||||||
Authors | Yu PY / Yang TJ / Chang YC / Wu HC / Hsu STD | |||||||||||||||
Funding support | Taiwan, 4 items
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Citation | Journal: To Be Published Title: Negative staining (NS)-EM structure of SARS-CoV-2 S-Kappa variant in complex with neutralizing antibody RBD-chAb-25 Authors: Yu PY / Yang TJ / Chang YC / Wu HC / Hsu STD | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31822.map.gz | 31.3 MB | EMDB map data format | |
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Header (meta data) | emd-31822-v30.xml emd-31822.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_31822.png | 27.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31822 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31822 | HTTPS FTP |
-Validation report
Summary document | emd_31822_validation.pdf.gz | 350.5 KB | Display | EMDB validaton report |
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Full document | emd_31822_full_validation.pdf.gz | 350.1 KB | Display | |
Data in XML | emd_31822_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_31822_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31822 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31822 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31822.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | NSEM structure of SARS-CoV-2 S-Kappa variant in complex with neutralizing antibody RBD-chAb-25 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies
Entire | Name: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies
Supramolecule | Name: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: S-Kappa variant, one neutralizing antibody RBD-chAb-25 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Experimental: 540 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |