[English] 日本語
Yorodumi- EMDB-34511: SARS-CoV-2 RBD in complex with the repebody A6 (Focused Refinement) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34511 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 RBD in complex with the repebody A6 (Focused Refinement) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Kim UJ / Yoo Y / Cho HS | |||||||||
Funding support | Korea, Republic Of, 1 items
| |||||||||
Citation | Journal: To Be Published Title: SARS-CoV-2 RBD in complex with the repebody A6 (Focused Refinement) Authors: Kim UJ / Yoo Y / Cho HS | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_34511.map.gz | 59.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-34511-v30.xml emd-34511.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34511_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_34511.png | 24.9 KB | ||
Filedesc metadata | emd-34511.cif.gz | 4.4 KB | ||
Others | emd_34511_half_map_1.map.gz emd_34511_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34511 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34511 | HTTPS FTP |
-Validation report
Summary document | emd_34511_validation.pdf.gz | 742 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_34511_full_validation.pdf.gz | 741.6 KB | Display | |
Data in XML | emd_34511_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_34511_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34511 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34511 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_34511.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.1834 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_34511_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_34511_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike protein in complex with neutralizing repebody A6
Entire | Name: SARS-CoV-2 Spike protein in complex with neutralizing repebody A6 |
---|---|
Components |
|
-Supramolecule #1: SARS-CoV-2 Spike protein in complex with neutralizing repebody A6
Supramolecule | Name: SARS-CoV-2 Spike protein in complex with neutralizing repebody A6 type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 180 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.47 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
Details: 20mM Tris-HCl, 200mM NaCl | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.11 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|