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Yorodumi- EMDB-12818: SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed con... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12818 | ||||||||||||||||||||||||
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Title | SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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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 / 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 2 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||
Authors | Toelzer C / Gupta K / Yadav SKN / Borucu U / Schaffitzel C / Berger I | ||||||||||||||||||||||||
Funding support | United Kingdom, 7 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2. Authors: Kapil Gupta / Christine Toelzer / Maia Kavanagh Williamson / Deborah K Shoemark / A Sofia F Oliveira / David A Matthews / Abdulaziz Almuqrin / Oskar Staufer / Sathish K N Yadav / Ufuk Borucu ...Authors: Kapil Gupta / Christine Toelzer / Maia Kavanagh Williamson / Deborah K Shoemark / A Sofia F Oliveira / David A Matthews / Abdulaziz Almuqrin / Oskar Staufer / Sathish K N Yadav / Ufuk Borucu / Frederic Garzoni / Daniel Fitzgerald / Joachim Spatz / Adrian J Mulholland / Andrew D Davidson / Christiane Schaffitzel / Imre Berger / Abstract: As the global burden of SARS-CoV-2 infections escalates, so does the evolution of viral variants with increased transmissibility and pathology. In addition to this entrenched diversity, RNA viruses ...As the global burden of SARS-CoV-2 infections escalates, so does the evolution of viral variants with increased transmissibility and pathology. In addition to this entrenched diversity, RNA viruses can also display genetic diversity within single infected hosts with co-existing viral variants evolving differently in distinct cell types. The BriSΔ variant, originally identified as a viral subpopulation from SARS-CoV-2 isolate hCoV-19/England/02/2020, comprises in the spike an eight amino-acid deletion encompassing a furin recognition motif and S1/S2 cleavage site. We elucidate the structure, function and molecular dynamics of this spike providing mechanistic insight into how the deletion correlates to viral cell tropism, ACE2 receptor binding and infectivity of this SARS-CoV-2 variant. Our results reveal long-range allosteric communication between functional domains that differ in the wild-type and the deletion variant and support a view of SARS-CoV-2 probing multiple evolutionary trajectories in distinct cell types within the same infected host. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12818.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-12818-v30.xml emd-12818.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12818_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_12818.png | 73.7 KB | ||
Masks | emd_12818_msk_1.map | 40.6 MB | Mask map | |
Others | emd_12818_half_map_1.map.gz emd_12818_half_map_2.map.gz | 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12818 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12818 | HTTPS FTP |
-Validation report
Summary document | emd_12818_validation.pdf.gz | 517.8 KB | Display | EMDB validaton report |
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Full document | emd_12818_full_validation.pdf.gz | 517.3 KB | Display | |
Data in XML | emd_12818_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_12818_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12818 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12818 | HTTPS FTP |
-Related structure data
Related structure data | 7od3MC 7odlC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12818.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12818_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12818_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12818_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed con...
Entire | Name: SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry |
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Components |
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-Supramolecule #1: SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed con...
Supramolecule | Name: SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-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: 140.510203 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLGVYYHKNN KSWMESEFRV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PINLVRDLPQ GFSALEPLVD LPIGINITRF QT LLALHRS YLTPGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRV QPTESI VRFPNITNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSF VIRGD EVRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYLYRL FRKSNLKPFE RDISTEIYQA GSTPC NGVE GFNCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGPKKSTNLV KNKCVNFNFN GLTGTGVLTE SNKKFL PFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGS NV FQTRAGCLIG AEHVNNSYEC DIPIGAGICA SYQTQTIASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILP V SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKDFGG FNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS S NFGAISSV LNDILSRLDK VEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YH LMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDV VIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQ GGGGS GGGGSGSGYI PEAPRDGQAY VRKDGEWVLL STFLGGGGGS GGGGSGSEQK LISEEDLGSG SGSHHHHHHH H |
-Macromolecule #2: LINOLEIC ACID
Macromolecule | Name: LINOLEIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: EIC |
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Molecular weight | Theoretical: 280.445 Da |
Chemical component information | ChemComp-EIC: |
-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: 33 / 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 | 1.4 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 8639 / Average exposure time: 11.0 sec. / Average electron dose: 63.8 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |