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- PDB-7z3z: Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z3z | ||||||
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Title | Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound | ||||||
![]() | Spike glycoprotein | ||||||
![]() | VIRAL PROTEIN / Spike / SARS-CoV2 / lipid / locked-in / conformation / COVID19 / RBD-down / therapeutics / vaccine / closed | ||||||
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: 3.1 Å | ||||||
![]() | Duyvesteyn, H.M.E. / Carrique, L. / Ren, J. / Stuart, D.I. / Fry, E.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The SARS-CoV-2 Spike harbours a lipid binding pocket which modulates stability of the prefusion trimer Authors: Duyvesteyn, H.M.E. / Carrique, L. / Ren, J. / Stuart, D.I. / Fry, E.E. / Zhao, Y. / Malinauskas, T. / Zhou, D. #1: ![]() Title: Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Authors: Huo, J. / Zhao, Y. / Ren, J. / Zhou, D. / Duyvesteyn, H.M.E. / Ginn, H.M. / Carrique, L. / Malinauskas, T. / Ruza, R.R. / Shah, P.N.M. / Tan, T.K. / Rijal, P. / Coombes, N. / Bewley, K.R. / ...Authors: Huo, J. / Zhao, Y. / Ren, J. / Zhou, D. / Duyvesteyn, H.M.E. / Ginn, H.M. / Carrique, L. / Malinauskas, T. / Ruza, R.R. / Shah, P.N.M. / Tan, T.K. / Rijal, P. / Coombes, N. / Bewley, K.R. / Tree, J.A. / Radecke, J. / Paterson, N.G. / Supasa, P. / Mongkolsapaya, J. / Screaton, G.R. / Carroll, M. / Townsend, A. / Fry, E.E. / Owens, R.J. / Stuart, D.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 929.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14481MC 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: 142408.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | 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 spike glycoprotein in locked conformation with lipid bound Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.142 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Details of virus | Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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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: 2600 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36000 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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