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Yorodumi- EMDB-60906: Structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with A... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60906 | |||||||||||||||||||||
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Title | Structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with ACE2 (2-up and 1-down state) | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Keywords | spike protein / glycoprotein / VIRUS / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN BINDING complex | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.39 Å | |||||||||||||||||||||
Authors | Yajima H / Anraku Y / Kita S / Kimura K / Maenaka K / Hashiguchi T | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1 Authors: Tamura T / Ito J / Uriu K / Zahradnik J / Kida I / Anraku Y / Nasser H / Shofa M / Oda Y / Lytras S / Nao N / Itakura Y / Deguchi S / Suzuki R / Wang L / Begum MM / Kita S / Yajima H / ...Authors: Tamura T / Ito J / Uriu K / Zahradnik J / Kida I / Anraku Y / Nasser H / Shofa M / Oda Y / Lytras S / Nao N / Itakura Y / Deguchi S / Suzuki R / Wang L / Begum MM / Kita S / Yajima H / Sasaki J / Sasaki-Tabata K / Shimizu R / Tsuda M / Kosugi Y / Fujita S / Pan L / Sauter D / Yoshimatsu K / Suzuki S / Asakura H / Nagashima M / Sadamasu K / Yoshimura K / Yamamoto Y / Nagamoto T / Schreiber G / Maenaka K / Hashiguchi T / Ikeda T / Fukuhara T / Saito A / Tanaka S / Matsuno K / Takayama K / Sato K | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60906.map.gz | 108.1 MB | EMDB map data format | |
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Header (meta data) | emd-60906-v30.xml emd-60906.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60906_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_60906.png | 102.4 KB | ||
Masks | emd_60906_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-60906.cif.gz | 5.3 KB | ||
Others | emd_60906_half_map_1.map.gz emd_60906_half_map_2.map.gz | 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60906 | HTTPS FTP |
-Validation report
Summary document | emd_60906_validation.pdf.gz | 1022.1 KB | Display | EMDB validaton report |
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Full document | emd_60906_full_validation.pdf.gz | 1021.7 KB | Display | |
Data in XML | emd_60906_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | emd_60906_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60906 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60906 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_60906.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.005 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_60906_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60906_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60906_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 JN.1 spike glycoprotein with ACE2
Entire | Name: SARS-CoV-2 JN.1 spike glycoprotein with ACE2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 JN.1 spike glycoprotein with ACE2
Supramolecule | Name: SARS-CoV-2 JN.1 spike glycoprotein with ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 600 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blotting time 5 s and blotting force 5.. |
-Electron microscopy
Microscope | TFS 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 K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 9018 / Average electron dose: 51.233 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: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
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
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |