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Yorodumi- EMDB-29395: Subtomogram average of HuCoV-NL63 spike protein from purified int... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29395 | ||||||||||||
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Title | Subtomogram average of HuCoV-NL63 spike protein from purified intact virions | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | coronavirus / glycoprotein / spike / cryoEM / cryoET / subtomogram average / VIRUS | ||||||||||||
Biological species | Human coronavirus NL63 | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.9 Å | ||||||||||||
Authors | Chen M / Chmielewski D / Schmid M / Jin J / Chiu W | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: A hinge glycan regulates spike bending and impacts coronavirus infectivity Authors: Chmielewski D / Wilson E / Pintilie G / Zhao P / Chen M / Schmid M / Simmons G / Wells L / Jin J / Singharoy A / Chiu W | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29395.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-29395-v30.xml emd-29395.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29395_fsc.xml | 6.8 KB | Display | FSC data file |
Images | emd_29395.png | 107.8 KB | ||
Filedesc metadata | emd-29395.cif.gz | 4.3 KB | ||
Others | emd_29395_half_map_1.map.gz emd_29395_half_map_2.map.gz | 14 MB 14.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29395 | HTTPS FTP |
-Validation report
Summary document | emd_29395_validation.pdf.gz | 773.2 KB | Display | EMDB validaton report |
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Full document | emd_29395_full_validation.pdf.gz | 772.8 KB | Display | |
Data in XML | emd_29395_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_29395_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29395 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29395 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29395.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29395_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29395_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human coronavirus NL63
Entire | Name: Human coronavirus NL63 |
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Components |
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-Supramolecule #1: Human coronavirus NL63
Supramolecule | Name: Human coronavirus NL63 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 277944 / Sci species name: Human coronavirus NL63 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.35 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |