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Yorodumi- PDB-8jym: Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jym | |||||||||||||||||||||
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Title | Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2) | |||||||||||||||||||||
Components | Spike glycoprotein | |||||||||||||||||||||
Keywords | VIRAL PROTEIN / spike protein / glycoprotein / VIRUS | |||||||||||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||||||||||||||
Authors | Yajima, H. / Anraku, Y. / Kita, S. / Kimura, K. / Sasaki, J. / Sasaki-Tabata, K. / Maenaka, K. / Hashiguchi, T. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: To Be Published Title: Virological characteristics of the SARS-CoV-2 XBB.1.5 variant 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, ...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, M.M. / 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jym.cif.gz | 227.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jym.ent.gz | 174.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jym_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8jym_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8jym_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 8jym_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/8jym ftp://data.pdbj.org/pub/pdb/validation_reports/jy/8jym | HTTPS FTP |
-Related structure data
Related structure data | 36726MC 8jykC 8jynC 8jyoC 8jypC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: C3 (3 fold cyclic)) |
-Components
#1: Protein | Mass: 138086.094 Da / Num. of mol.: 1 Mutation: F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SARS-CoV-2 XBB1.5 spike glycoprotein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.42 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: blotting time 5 s and blotting force 5. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 3522 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1201208 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67040 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8IOT Accession code: 8IOT / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 139.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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