+Open data
-Basic information
Entry | Database: PDB / ID: 8x4h | ||||||
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Title | SARS-CoV-2 JN.1 Spike | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / Timer | ||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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: 3.65 Å | ||||||
Authors | Yue, C. / Liu, P. | ||||||
Funding support | 1items
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Citation | Journal: Natl Sci Rev / Year: 2024 Title: Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity Authors: Liu, P. / Yue, C. / Meng, B. / Xiao, T. / Yang, S. / Liu, S. / Jian, F. / Zhu, Q. / Yu, Y. / Ren, Y. / Wang, P. / Li, Y. / Wang, J. / Mao, X. / Shao, F. / Wang, Y. / Gupta, R.K. / Cao, Y. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8x4h.cif.gz | 580.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8x4h.ent.gz | 473.8 KB | Display | PDB format |
PDBx/mmJSON format | 8x4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8x4h_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8x4h_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8x4h_validation.xml.gz | 100 KB | Display | |
Data in CIF | 8x4h_validation.cif.gz | 146.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/8x4h ftp://data.pdbj.org/pub/pdb/validation_reports/x4/8x4h | HTTPS FTP |
-Related structure data
Related structure data | 38049MC 8whsC 8whuC 8whvC 8whwC 8whzC 8x4zC 8x50C 8x55C 8x56C 8x5qC 8x5rC 8xurC 8xusC 8xutC 8xuuC 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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-Components
#1: Protein | Mass: 134015.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Strain: Omicron/JN.1 / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-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: Severe acute respiratory syndrome coronavirus 2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 223122 / Symmetry type: POINT | ||||||||||||||||||||||||
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