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Yorodumi- EMDB-15475: Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spik... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15475 | ||||||||||||||||||
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Title | Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein | ||||||||||||||||||
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Sample |
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Keywords | Ancestor / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 | Severe acute respiratory syndrome coronavirus / Tequatrovirus T4 | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.59 Å | ||||||||||||||||||
Authors | Hueting D / Schriever K / Wallden K / Andrell J / Syren PO | ||||||||||||||||||
Funding support | Sweden, European Union, 5 items
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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 PO | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15475.map.gz | 204.1 MB | EMDB map data format | |
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Header (meta data) | emd-15475-v30.xml emd-15475.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15475_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_15475.png | 26.6 KB | ||
Masks | emd_15475_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-15475.cif.gz | 7.5 KB | ||
Others | emd_15475_half_map_1.map.gz emd_15475_half_map_2.map.gz | 200.8 MB 200.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15475 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15475 | HTTPS FTP |
-Validation report
Summary document | emd_15475_validation.pdf.gz | 974.8 KB | Display | EMDB validaton report |
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Full document | emd_15475_full_validation.pdf.gz | 974.4 KB | Display | |
Data in XML | emd_15475_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | emd_15475_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15475 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15475 | HTTPS FTP |
-Related structure data
Related structure data | 8ajaMC 8ajlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15475.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15475_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15475_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15475_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ancestral S-protein of coronaviruses related to SARS-CoV-2
Entire | Name: Ancestral S-protein of coronaviruses related to SARS-CoV-2 |
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Components |
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-Supramolecule #1: Ancestral S-protein of coronaviruses related to SARS-CoV-2
Supramolecule | Name: 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. |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: 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 |
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Source (natural) | Organism: Tequatrovirus T4 |
Molecular weight | Theoretical: 137.212609 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 39 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: 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. | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.11 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |