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- PDB-8vkp: Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vkp | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) | ||||||
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Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, X. / Mannar, D. / Saville, J. / Poloni, C. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. ...Zhu, X. / Mannar, D. / Saville, J. / Poloni, C. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. / Cook, L. / Steiner, T.S. / Subramaniam, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition Authors: Mannar, D. / Saville, J. / Poloni, C. / Zhu, X. / Bezeruk, A. / Tidey, K. / Ahmed, S. / Tuttle, K. / Vahdatihassani, F. / Cholak, S. / Cook, L. / Steiner, T.S. / Subramaniam, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.5 KB | Display | ![]() |
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PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 43325MC ![]() 8vkkC ![]() 8vklC ![]() 8vkmC ![]() 8vknC ![]() 8vkoC 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: 22580.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: XBB.1.5 RBD Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 70386.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: SARS-CoV-2 XBB.1.5 spike protein trimer bound to 3 human ACE2 molecules Type: COMPLEX / Entity ID: #1-#2 / 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![]() ![]() |
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: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction![]() | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243720 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 102.02 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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