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- EMDB-15475: Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spik... -

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Basic information

Entry
Database: EMDB / ID: EMD-15475
TitleStructure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein
Map data
Sample
  • Complex: Ancestral S-protein of coronaviruses related to SARS-CoV-2
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAncestor / Spike / Coronavirus / Scaffold / S-protein / Protein Engineering / BIOSYNTHETIC PROTEIN
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 / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsHueting D / Schriever K / Wallden K / Andrell J / Syren PO
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Other government2019-700
Other governmentSNIC 2021/5-70
The Swedish Foundation for Strategic ResearchFFF20-0027 Sweden
European Union (EU)ATAC, 101003650European Union
Knut and Alice Wallenberg FoundationSciLifeLab/KAW national COVID-19 research program project grant 2020 (KAW 2020.0182) Sweden
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 PO
History
DepositionJul 27, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15475.png

Downloads & links

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Map

FileDownload / File: emd_15475.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 384 pix.
= 426.24 Å		1.11 Å/pix.
x 384 pix.
= 426.24 Å		1.11 Å/pix.
x 384 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-3.3500786 - 5.7358475
Average (Standard dev.)-0.00053288054 (±0.110702045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15475_msk_1.map
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Half map: #1

Fileemd_15475_half_map_1.map
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Histogram

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Half map: #2

Fileemd_15475_half_map_2.map
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Sample components

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Entire : Ancestral S-protein of coronaviruses related to SARS-CoV-2

EntireName: Ancestral S-protein of coronaviruses related to SARS-CoV-2
Components
  • Complex: Ancestral S-protein of coronaviruses related to SARS-CoV-2
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ancestral S-protein of coronaviruses related to SARS-CoV-2

SupramoleculeName: Ancestral S-protein of coronaviruses related to SARS-CoV-2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ancestral coronavirus generated by Ancestral sequence reconstruction expressed in human cells.
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1
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
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 137.212609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TCGTISNKTP PNMNQFSSSR RGVYYPDDIF RSDVLHLTQD YFLPFNSNVT RYLSLNADSN RIVRFDNPIL PFGDGIYFAA TEKSNVIRG WIFGSTLDNT SQSAIIVNNS THIIIKVCNF QLCDDPMFTV SRGQHYKTWV YTNARNCTYE YVSKSFQLDV S EKNGNFKH ...String:
TCGTISNKTP PNMNQFSSSR RGVYYPDDIF RSDVLHLTQD YFLPFNSNVT RYLSLNADSN RIVRFDNPIL PFGDGIYFAA TEKSNVIRG WIFGSTLDNT SQSAIIVNNS THIIIKVCNF QLCDDPMFTV SRGQHYKTWV YTNARNCTYE YVSKSFQLDV S EKNGNFKH LREFVFKNVD GFLHVYSAYE PIDLARGLPS GFSVLKPILK LPLGINITSF RVVMTMFSPT TSNWLAESAA YF VGYLKPT TFMLKFNENG TITDAVDCSQ DPLSELKCTL KSFNVEKGIY QTSNFRVSPT QEVVRFPNIT NLCPFDKVFN ATR FPSVYA WERTKISDCV ADYTVLYNST SFSTFKCYGV SPSKLIDLCF TSVYADTFLI RSSEVRQVAP GQTGVIADYN YKLP DDFTG CVIAWNTAKQ DAGNYYYRSH RKTKLKPFER DLSNSDENGV RTLSTYDFNP NVPIEYQATR VVVLSFELLN APATV CGPK LSTQLVKNQC VNFNFNGLKG TGVLTDSSKR FQSFQQFGRD ASDFTDSVRD PQTLEILDIS PCSFGGVSVI TPGTNA SSE VAVLYQDVNC TDVPTAIHAD QLTPAWRVYS TGVNVFQTQA GCLIGAEHVN ASYECDIPIG AGICASYHTA STLRSTG QK SIVAYTMSLG AENSIAYANN SIAIPTNFSI SVTTEVMPVS MAKTSVDCTM YICGDSQECS NLLLQYGSFC TQLNRALT G IAIEQDKNTQ EVFAQVKQMY KTPAIKDFGG FNFSQILPDP SKPTKRSFIE DLLFNKVTLA DAGFMKQYGE CLGDISARD LICAQKFNGL TVLPPLLTDE MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQES LTTTSTALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLDKV EAEVQIDRLI TGRLQSLQTY V TQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PHGVVFLHVT YVPSQERNFT TAPAICHEGK AY FPREGVF VSNGTSWFIT QRNFYSPQII TTDNTFVAGN CDVVIGIINN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGD ISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQGSGYIP EAPRDGQAYV RKDGEWVLLS TFLGTSLEVL FQGP GHHHH HHHHSAWSHP QFEKGGGSGG GGSGGSAWSH PQFEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClSodium chloridesodium chloride
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: Grids were glow discharged with 20mA for 60s in GlowQube system.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.11 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2555520
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zoz


Details: 7BNN was also used as startup model.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: ISOLDE (ver. 1.1) / Number images used: 959111
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6zoz

source_name: PDB, initial_model_type: experimental model

7bnn

source_name: PDB, initial_model_type: experimental model
Output model

PDB-8aja:
Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein

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