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Yorodumi- EMDB-28531: Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD D... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28531 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation | |||||||||
Map data | Designed SARS-CoV-2 Spike antigen, S2D14, with three RBDs in the down conformation. | |||||||||
Sample |
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Keywords | Glycoprotein / trimer / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 / 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 | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Williams JA / Harshbarger W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural and computational design of a SARS-CoV-2 spike antigen with improved expression and immunogenicity. Authors: James A Williams / Marco Biancucci / Laura Lessen / Sai Tian / Ankita Balsaraf / Lynn Chen / Chelsy Chesterman / Giulietta Maruggi / Sarah Vandepaer / Ying Huang / Corey P Mallett / Ann- ...Authors: James A Williams / Marco Biancucci / Laura Lessen / Sai Tian / Ankita Balsaraf / Lynn Chen / Chelsy Chesterman / Giulietta Maruggi / Sarah Vandepaer / Ying Huang / Corey P Mallett / Ann-Muriel Steff / Matthew James Bottomley / Enrico Malito / Newton Wahome / Wayne D Harshbarger / Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern challenge the efficacy of approved vaccines, emphasizing the need for updated spike antigens. Here, we use an ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern challenge the efficacy of approved vaccines, emphasizing the need for updated spike antigens. Here, we use an evolutionary-based design aimed at boosting protein expression levels of S-2P and improving immunogenic outcomes in mice. Thirty-six prototype antigens were generated in silico and 15 were produced for biochemical analysis. S2D14, which contains 20 computationally designed mutations within the S2 domain and a rationally engineered D614G mutation in the SD2 domain, has an ~11-fold increase in protein yield and retains RBD antigenicity. Cryo-electron microscopy structures reveal a mixture of populations in various RBD conformational states. Vaccination of mice with adjuvanted S2D14 elicited higher cross-neutralizing antibody titers than adjuvanted S-2P against the SARS-CoV-2 Wuhan strain and four variants of concern. S2D14 may be a useful scaffold or tool for the design of future coronavirus vaccines, and the approaches used for the design of S2D14 may be broadly applicable to streamline vaccine discovery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28531.map.gz | 480.8 MB | EMDB map data format | |
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Header (meta data) | emd-28531-v30.xml emd-28531.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28531_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_28531.png | 142 KB | ||
Others | emd_28531_half_map_1.map.gz emd_28531_half_map_2.map.gz | 410.7 MB 410.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28531 | HTTPS FTP |
-Related structure data
Related structure data | 8epnMC 8eppC 8epqC 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_28531.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Designed SARS-CoV-2 Spike antigen, S2D14, with three RBDs in the down conformation. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.67 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half1 - Designed SARS-CoV-2 Spike antigen, S2D14, with...
File | emd_28531_half_map_1.map | ||||||||||||
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Annotation | Half1 - Designed SARS-CoV-2 Spike antigen, S2D14, with three RBDs in the down conformation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 - Designed SARS-CoV-2 Spike antigen, S2D14, with...
File | emd_28531_half_map_2.map | ||||||||||||
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Annotation | Half1 - Designed SARS-CoV-2 Spike antigen, S2D14, with three RBDs in the down conformation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike trimer
Entire | Name: SARS-CoV-2 Spike trimer |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike trimer
Supramolecule | Name: SARS-CoV-2 Spike trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 550 KDa |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 123.913258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AIHVSGTNGT KRFDNPVLPF NDGVYFASTE KSNIIRGWIF GTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLGVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN F KNLREFVF ...String: AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH AIHVSGTNGT KRFDNPVLPF NDGVYFASTE KSNIIRGWIF GTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLGVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN F KNLREFVF KNIDGYFKIY SKHTPINLVR DLPQGFSALE PLVDLPIGIN ITRFQTLLAL HRSYLTPGDS SSGWTAGAAA YY VGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLCPFGEVFN ATR FASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADYN YKLP DDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP LQSYGFQPTN GVGYQ PYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILD ITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTRAGC LIGAEHVNNS YECDIPI GA GICASYQTQT NSPGSASSVA SQSIIAYTMS LGEENSVAYS NNSIAIPTNF TISVTTEIIP VSMQKVSVDC TMYICGDS E ECSNLLLQYG SFCTQLNRAL HEIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQILP DPSKPSKRSA IEDLLFNKV TLADAGFIKG YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAAYTSA LLAGTITAGW TFGAGAALQI PFAMQMAYRF NGIGVTQNV LYENQKLIAN QFNKAIGKIQ DGLSSTASAL GKLQDVVNQN AQALNTLVKQ LSSNFGAISS VLNDILSRLD P PEAEVQID RLINGRLQAL NTYVTQQLIR AAEIRASANL AAEKMSECVL GQSKRVDFCG KGYHLMSFPQ SAPHGVVFLH VT YVPTQYK NFTTAPAICH NGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GDCDVVIGIV NNTVYDPLQP ELD S |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 15 / 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 | 0.40 mg/mL |
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Buffer | pH: 7.5 / Details: 10mM Tris + 150mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 6169 / Average exposure time: 12.21 sec. / Average electron dose: 43.45 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |