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Open data
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Basic information
Entry | Database: PDB / ID: 6z97 | ||||||||||||
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Title | Structure of the prefusion SARS-CoV-2 spike glycoprotein | ||||||||||||
![]() | Spike glycoprotein,Fibritin | ||||||||||||
![]() | VIRAL PROTEIN / SARS-CoV-2 Spike glycoprotein / RBD / CR3022 / complex | ||||||||||||
Function / homology | ![]() virion component / 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 ...virion component / 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: 3.4 Å | ||||||||||||
![]() | Duyvesteyn, H.M.E. / Ren, J. / Zhao, Y. / Zhou, D. / Huo, J. / Carrique, L. / Malinauskas, T. / Ruza, R.R. / Shah, P.N.M. / Fry, E.E. ...Duyvesteyn, H.M.E. / Ren, J. / Zhao, Y. / Zhou, D. / Huo, J. / Carrique, L. / Malinauskas, T. / Ruza, R.R. / Shah, P.N.M. / Fry, E.E. / Owens, R. / Stuart, D.I. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike. Authors: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila ...Authors: Jiandong Huo / Yuguang Zhao / Jingshan Ren / Daming Zhou / Helen M E Duyvesteyn / Helen M Ginn / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Naomi Coombes / Kevin R Bewley / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles Carroll / Alain Townsend / Elizabeth E Fry / Raymond J Owens / David I Stuart / ![]() ![]() Abstract: There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes ...There are as yet no licensed therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2, initiating conformational changes that drive membrane fusion. We find that the monoclonal antibody CR3022 binds the RBD tightly, neutralizing SARS-CoV-2, and report the crystal structure at 2.4 Å of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilizing CR3022 epitope is inaccessible in the prefusion spike, suggesting that CR3022 binding facilitates conversion to the fusion-incompetent post-fusion state. Cryogenic electron microscopy (cryo-EM) analysis confirms that incubation of spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope could be useful therapeutically, possibly in synergy with an antibody that blocks receptor attachment. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 957.2 KB | Display | ![]() |
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PDB format | ![]() | 821.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 79.6 KB | Display | |
Data in CIF | ![]() | 119.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11119MC ![]() 6ylaC ![]() 6ym0C ![]() 6yorC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 142399.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2, wac / 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 / 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 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
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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 |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.1_3865: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328000 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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