[English] 日本語
Yorodumi- EMDB-22147: Negative stain EM map of SARS-COV-2 spike protein closed RBD (tri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22147 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Negative stain EM map of SARS-COV-2 spike protein closed RBD (trimer) with Fab COV2-2096 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Binshtein E / Crowe JE | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Negative stain EM map of SARS-COV-2 spike protein closed RBD (trimer) with Fab COV2-2096 Authors: Binshtein E | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22147.map.gz | 4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22147-v30.xml emd-22147.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_22147.png | 26.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22147 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22147 | HTTPS FTP |
-Validation report
Summary document | emd_22147_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22147_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_22147_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22147 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22147 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22147.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 4.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : SARS-CoV-2 spike protein (trimer) with Fab COV2-2096
Entire | Name: SARS-CoV-2 spike protein (trimer) with Fab COV2-2096 |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 spike protein (trimer) with Fab COV2-2096
Supramolecule | Name: SARS-CoV-2 spike protein (trimer) with Fab COV2-2096 / type: complex / ID: 1 / Parent: 0 |
---|
-Supramolecule #2: SARS-COV-2 spike protein (trimer)
Supramolecule | Name: SARS-COV-2 spike protein (trimer) / type: complex / ID: 2 / Parent: 1 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: Fab COV2-2096
Supramolecule | Name: Fab COV2-2096 / type: complex / ID: 3 / Parent: 1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||
Staining | Type: NEGATIVE / Material: UF | |||||||||
Grid | Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 562 / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |