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- PDB-8xm5: Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xm5 | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state | ||||||
![]() | Spike glycoprotein | ||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 / Omicron / EG.5 / 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 / membrane fusion / Attachment and Entry / 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å | ||||||
![]() | Li, L.J. / Gu, Y.H. / Shi, K.Y. / Qi, J.X. / Gao, G.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants Authors: Li, L.J. / Xu, Z.P. / Liu, K.F. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 618.2 KB | Display | ![]() |
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PDB format | ![]() | 492.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 94.3 KB | Display | |
Data in CIF | ![]() | 138 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 38463MC ![]() 8xlvC ![]() 8xmgC ![]() 8xmtC ![]() 8xn2C ![]() 8xn3C ![]() 8xn5C ![]() 8xnkC 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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Components
#1: Protein | Mass: 141066.750 Da / Num. of mol.: 3 / Mutation: F817P, A892P, A899P, A942P, K986P, V987P Source method: isolated from a genetically manipulated source Details: Omicron EG.5 Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #2: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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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 Omicron EG.5 spike protein(6P), RBD-closed state Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473611 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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