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Yorodumi- PDB-8aja: Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spik... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aja | ||||||||||||||||||
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Title | Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein | ||||||||||||||||||
Components | Spike glycoprotein,Fibritin | ||||||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Ancestor / Spike / Coronavirus / Scaffold / S-protein / Protein Engineering | ||||||||||||||||||
Function / homology | Function and homology information 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 | Severe acute respiratory syndrome coronavirus Tequatrovirus T4 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å | ||||||||||||||||||
Authors | Hueting, D. / Schriever, K. / Wallden, K. / Andrell, J. / Syren, P.O. | ||||||||||||||||||
Funding support | Sweden, European Union, 5items
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Citation | Journal: Nat Commun / Year: 2023 Title: Design, structure and plasma binding of ancestral β-CoV scaffold antigens. Authors: David Hueting / Karen Schriever / Rui Sun / Stelios Vlachiotis / Fanglei Zuo / Likun Du / Helena Persson / Camilla Hofström / Mats Ohlin / Karin Walldén / Marcus Buggert / Lennart ...Authors: David Hueting / Karen Schriever / Rui Sun / Stelios Vlachiotis / Fanglei Zuo / Likun Du / Helena Persson / Camilla Hofström / Mats Ohlin / Karin Walldén / Marcus Buggert / Lennart Hammarström / Harold Marcotte / Qiang Pan-Hammarström / Juni Andréll / Per-Olof Syrén / Abstract: We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma ...We report the application of ancestral sequence reconstruction on coronavirus spike protein, resulting in stable and highly soluble ancestral scaffold antigens (AnSAs). The AnSAs interact with plasma of patients recovered from COVID-19 but do not bind to the human angiotensin-converting enzyme 2 (ACE2) receptor. Cryo-EM analysis of the AnSAs yield high resolution structures (2.6-2.8 Å) indicating a closed pre-fusion conformation in which all three receptor-binding domains (RBDs) are facing downwards. The structures reveal an intricate hydrogen-bonding network mediated by well-resolved loops, both within and across monomers, tethering the N-terminal domain and RBD together. We show that AnSA-5 can induce and boost a broad-spectrum immune response against the wild-type RBD as well as circulating variants of concern in an immune organoid model derived from tonsils. Finally, we highlight how AnSAs are potent scaffolds by replacing the ancestral RBD with the wild-type sequence, which restores ACE2 binding and increases the interaction with convalescent plasma. #1: Journal: Res Sq / Year: 2023 Title: Design, structure and plasma binding of ancestral beta-CoV scaffold antigens Authors: Hueting, D. / Schriever, K. / Zuo, F. / Du, L. / Persson, H. / Hofstrom, C. / Ohlin, M. / Wallden, K. / Hammarstrom, L. / Marcotte, H. / Pan-Hammarstrom, Q. / Andrell, J. / Syren, P.O. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aja.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8aja.ent.gz | 908.5 KB | Display | PDB format |
PDBx/mmJSON format | 8aja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aja_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8aja_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8aja_validation.xml.gz | 94.2 KB | Display | |
Data in CIF | 8aja_validation.cif.gz | 145.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/8aja ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8aja | HTTPS FTP |
-Related structure data
Related structure data | 15475MC 8ajlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 137212.609 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: AnSA-5 With His-Tag and Twin-Strep-tag and SARS-CoV-2 signaling peptide 1-19 Signaling peptide 653-660 No density 1119 onwards, no density and expression and purification tag,AnSA-5 With His- ...Details: AnSA-5 With His-Tag and Twin-Strep-tag and SARS-CoV-2 signaling peptide 1-19 Signaling peptide 653-660 No density 1119 onwards, no density and expression and purification tag,AnSA-5 With His-Tag and Twin-Strep-tag and SARS-CoV-2 signaling peptide 1-19 Signaling peptide 653-660 No density 1119 onwards, no density and expression and purification tag,AnSA-5 With His-Tag and Twin-Strep-tag and SARS-CoV-2 signaling peptide 1-19 Signaling peptide 653-660 No density 1119 onwards, no density and expression and purification tag,AnSA-5 With His-Tag and Twin-Strep-tag and SARS-CoV-2 signaling peptide 1-19 Signaling peptide 653-660 No density 1119 onwards, no density and expression and purification tag Source: (gene. exp.) Severe acute respiratory syndrome coronavirus, (gene. exp.) Tequatrovirus T4 Gene: S, 2, wac / Plasmid: pMx series / Production host: Homo sapiens (human) / Strain (production host): Expi293F / References: UniProt: P0DTC2, UniProt: P10104 #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 |
-Sample preparation
Component | Name: Ancestral S-protein of coronaviruses related to SARS-CoV-2 Type: COMPLEX Details: Ancestral coronavirus generated by Ancestral sequence reconstruction expressed in human cells. Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Details: Grids were glow discharged with 20mA for 60s in GlowQube system. Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.11 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-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 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2555520 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 959111 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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