+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14717 | ||||||||||||||||||||||||
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Title | SARS CoV Spike protein, Closed C3 conformation | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | SARS-CoV / VIRAL PROTEIN / Spike | ||||||||||||||||||||||||
Function / homology | Function and homology information Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / virion component / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / virion component / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / symbiont-mediated-mediated suppression of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome-related coronavirus / Enterobacteria phage T4 (virus) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.48 Å | ||||||||||||||||||||||||
Authors | Toelzer C / Gupta K / Yadav SKN / Buzas D / Borucu U / Schaffitzel C / Berger I | ||||||||||||||||||||||||
Funding support | United Kingdom, 7 items
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Citation | Journal: Sci Adv / Year: 2022 Title: The free fatty acid-binding pocket is a conserved hallmark in pathogenic β-coronavirus spike proteins from SARS-CoV to Omicron. Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Lorna Hodgson / Maia Kavanagh Williamson / Dora Buzas / Ufuk Borucu / Kyle Powers / Richard Stenner / Kate Vasileiou / Frederic Garzoni ...Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Lorna Hodgson / Maia Kavanagh Williamson / Dora Buzas / Ufuk Borucu / Kyle Powers / Richard Stenner / Kate Vasileiou / Frederic Garzoni / Daniel Fitzgerald / Christine Payré / Gunjan Gautam / Gérard Lambeau / Andrew D Davidson / Paul Verkade / Martin Frank / Imre Berger / Christiane Schaffitzel / Abstract: As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S ...As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor binding domain (RBD) comprises a free fatty acid (FFA)-binding pocket. FFA binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic β-coronaviruses (β-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2, and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold-causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation, while the open, infectious conformation is devoid of LA. Electron tomography of SARS-CoV-2-infected cells reveals that LA treatment inhibits viral replication, resulting in fewer deformed virions. Our results establish FFA binding as a hallmark of pathogenic β-CoV infection and replication, setting the stage for FFA-based antiviral strategies to overcome COVID-19. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14717.map.gz | 6.2 MB | EMDB map data format | |
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Header (meta data) | emd-14717-v30.xml emd-14717.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14717_fsc.xml | 7.8 KB | Display | FSC data file |
Images | emd_14717.png | 34.6 KB | ||
Masks | emd_14717_msk_1.map | 40.6 MB | Mask map | |
Filedesc metadata | emd-14717.cif.gz | 7.2 KB | ||
Others | emd_14717_half_map_1.map.gz emd_14717_half_map_2.map.gz | 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14717 | HTTPS FTP |
-Validation report
Summary document | emd_14717_validation.pdf.gz | 836.6 KB | Display | EMDB validaton report |
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Full document | emd_14717_full_validation.pdf.gz | 836.2 KB | Display | |
Data in XML | emd_14717_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_14717_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14717 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14717 | HTTPS FTP |
-Related structure data
Related structure data | 7zh1MC 7zh2C 7zh5C 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_14717.map.gz / Format: CCP4 / Size: 40.6 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14717_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14717_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14717_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS CoV Spike protein, Closed conformation, C3 symmetry
Entire | Name: SARS CoV Spike protein, Closed conformation, C3 symmetry |
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Components |
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-Supramolecule #1: SARS CoV Spike protein, Closed conformation, C3 symmetry
Supramolecule | Name: SARS CoV Spike protein, Closed conformation, C3 symmetry type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome-related coronavirus |
Molecular weight | Theoretical: 414 KDa |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) |
Molecular weight | Theoretical: 138.203188 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MVSAIVLYVL LAAAAHSAFA SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIP FKDGIYFAAT EKSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI F DNAFNCTF ...String: MVSAIVLYVL LAAAAHSAFA SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIP FKDGIYFAAT EKSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI F DNAFNCTF EYISDAFSLD VSEKSGNFKH LREFVFKNKD GFLYVYKGYQ PIDVVRDLPS GFNTLKPIFK LPLGINITNF RA ILTAFSP AQDTWGTSAA AYFVGYLKPT TFMLKYDENG TITDAVDCSQ NPLAELKCSV KSFEIDKGIY QTSNFRVVPS GDV VRFPNI TNLCPFGEVF NATKFPSVYA WERKKISNCV ADYSVLYNST FFSTFKCYGV SATKLNDLCF SNVYADSFVV KGDD VRQIA PGQTGVIADY NYKLPDDFMG CVLAWNTRNI DATSTGNYNY KYRYLRHGKL RPFERDISNV PFSPDGKPCT PPALN CYWP LNDYGFYTTT GIGYQPYRVV VLSFELLNAP ATVCGPKLST DLIKNQCVNF NFNGLTGTGV LTPSSKRFQP FQQFGR DVS DFTDSVRDPK TSEILDISPC SFGGVSVITP GTNASSEVAV LYQDVNCTDV STAIHADQLT PAWRIYSTGN NVFQTQA GC LIGAEHVDTS YECDIPIGAG ICASYHTVSL LRSTSQKSIV AYTMSLGADS SIAYSNNTIA IPTNFSISIT TEVMPVSM A KTSVDCNMYI CGDSTECANL LLQYGSFCTQ LNRALSGIAA EQDRNTREVF AQVKQMYKTP TLKYFGGFNF SQILPDPLK PTKRSFIEDL LFNKVTLADA GFMKQYGECL GDINARDLIC AQKFNGLTVL PPLLTDDMIA AYTAALVSGT ATAGWTFGAG AALQIPFAM QMAYRFNGIG VTQNVLYENQ KQIANQFNKA ISQIQESLTT TSTALGKLQD VVNQNAQALN TLVKQLSSNF G AISSVLND ILSRLDKVEA EVQIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MS FPQAAPH GVVFLHVTYV PSQERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD NTFVSGNCDV VIG IINNTV YDPLQPELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QYIK PSGRL VPRGSPGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGHHHH HH UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #3: LINOLEIC ACID
Macromolecule | Name: LINOLEIC ACID / type: ligand / ID: 3 / Number of copies: 3 / Formula: EIC |
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Molecular weight | Theoretical: 280.445 Da |
Chemical component information | ChemComp-EIC: |
-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: 30 / 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 | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-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: 6600 / Average exposure time: 12.0 sec. / Average electron dose: 62.65 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 |