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Open data
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Basic information
Entry | Database: PDB / ID: 8hri | ||||||
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Title | SARS-CoV-2 Delta variant spike protein | ||||||
![]() | Spike glycoprotein | ||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / Delta / Spike protein | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
![]() | Xu, J. / Cheng, H. / Liu, N. / Wang, H.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Self-assembled monolayers guided free-standing atomic-crystal/molecule superstructure Authors: Zheng, L. / Xu, J. / Wang, W. / Gao, X. / Liu, N. / Wang, H.W. / Peng, H.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 615.8 KB | Display | ![]() |
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PDB format | ![]() | 495.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34974MC ![]() 8hrjC ![]() 8hrkC ![]() 8hrlC ![]() 8hrmC ![]() 8hrnC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 138842.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: For issue of poor atom inclusion, the depositor stated 'we have tried our best to fit the coordinates in the density map of spike via rigid-body dock. However, the flexibility of RBD makes ...Details: For issue of poor atom inclusion, the depositor stated 'we have tried our best to fit the coordinates in the density map of spike via rigid-body dock. However, the flexibility of RBD makes it hard to fit, which seems to be general for spike proteins.' Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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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 |
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Sample preparation
Component | Name: SARS-CoV-2 Delta variant spike protein / Type: COMPLEX / Details: on graphene membranes / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 167167 / Symmetry type: POINT | ||||||||||||||||||||||||
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