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Yorodumi- EMDB-30669: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutraliz... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30669 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-25 | ||||||||||||||||||||||||||||||
Map data | SARS-CoV-2 Spike in complex with chAb-25 | ||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||||||||||||||
Authors | Yang TJ / Yu PY / Wu HC / Hsu STD | ||||||||||||||||||||||||||||||
Funding support | Taiwan, 9 items
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Citation | Journal: To be published Title: Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-25 Authors: Hsu STD / Wu HC / Yang TJ / Yu PY | ||||||||||||||||||||||||||||||
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_30669.map.gz | 204.1 MB | EMDB map data format | |
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Header (meta data) | emd-30669-v30.xml emd-30669.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30669_fsc.xml | 17.6 KB | Display | FSC data file |
Images | emd_30669.png | 47.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30669 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30669 | HTTPS FTP |
-Validation report
Summary document | emd_30669_validation.pdf.gz | 367.9 KB | Display | EMDB validaton report |
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Full document | emd_30669_full_validation.pdf.gz | 367.5 KB | Display | |
Data in XML | emd_30669_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_30669_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30669 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30669 | HTTPS FTP |
-Related structure data
Related structure data | 7ej4MC 7ej5C 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_30669.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 Spike in complex with chAb-25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 spike glycoprotein in complex with a neutralizing anti...
Entire | Name: SARS-CoV-2 spike glycoprotein in complex with a neutralizing antibody chAb-25 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with a neutralizing anti...
Supramolecule | Name: SARS-CoV-2 spike glycoprotein in complex with a neutralizing antibody chAb-25 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 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 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |