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Yorodumi- EMDB-12082: Cryo-EM map of the SARS-CoV-2 spike protein in complex with sybod... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12082 | ||||||||||||
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Title | Cryo-EM map of the SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 3up conformation. | ||||||||||||
Map data | Cryo-EM map of the SARS-CoV-2 spike protein in complex with Sb#15 and Sb#68 at 2.98 A resolution in a 3up conformation. Map was sharpened with a b factor of 99 A2 | ||||||||||||
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 / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||||||||
Authors | Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P ...Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / Thavarasah S / Zimmer G / Slotboom DJ / Paulino C / Plattet P / Seeger MA | ||||||||||||
Funding support | Netherlands, Switzerland, 3 items
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Citation | Journal: bioRxiv / Year: 2020 Title: Highly potent bispecific sybodies neutralize SARS-CoV-2 Authors: Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / ...Authors: Walter JD / Hutter CAJ / Garaeva AA / Scherer M / Zimmermann I / Wyss M / Rheinberger J / Ruedin Y / Earp JC / Egloff P / Sorgenfrei M / Huerlimann LM / Gonda I / Meier G / Remm S / Thavarasah S / Zimmer G / Slotboom DJ / Paulino C / Plattet P / Seeger MA | ||||||||||||
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_12082.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-12082-v30.xml emd-12082.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
Images | emd_12082.png | 71.2 KB | ||
Masks | emd_12082_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12082_half_map_1.map.gz emd_12082_half_map_2.map.gz | 226.4 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12082 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12082 | HTTPS FTP |
-Validation report
Summary document | emd_12082_validation.pdf.gz | 424.9 KB | Display | EMDB validaton report |
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Full document | emd_12082_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | emd_12082_validation.xml.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12082 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12082 | HTTPS FTP |
-Related structure data
Related structure data | 7p77M 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_12082.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the SARS-CoV-2 spike protein in complex with Sb#15 and Sb#68 at 2.98 A resolution in a 3up conformation. Map was sharpened with a b factor of 99 A2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.012 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_12082_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map 2 used for post processing step and...
File | emd_12082_half_map_1.map | ||||||||||||
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Annotation | half-map 2 used for post processing step and FSC resolution calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 1 used for post processing step and...
File | emd_12082_half_map_2.map | ||||||||||||
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Annotation | half-map 1 used for post processing step and FSC resolution calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68
Entire | Name: SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68
Supramolecule | Name: SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: SARS-CoV-2 spike protein
Supramolecule | Name: SARS-CoV-2 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: sybody#15 and sybody#68
Supramolecule | Name: sybody#15 and sybody#68 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: synthetic construct (others) |
-Macromolecule #1: SARS-CoV-2 spike protein
Macromolecule | Name: SARS-CoV-2 spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDGV YFASTEKSNI IRGWIFGTTL DSKTQSLLIV NNATNVVIKV CEFQFCNDPF LGVYYHKNNK SWMESEFRVY SSANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NITNLCPFGE VFNATRFASV YAWNRKRISN CVADYSVLYN SASFSTFKCY GVSPTKLNDL CFTNVYADSF VIRGDEVRQI APGQTGKIAD YNYKLPDDFT GCVIAWNSNN LDSKVGGNYN YLYRLFRKSN LKPFERDIST EIYQAGSTPC NGVEGFNCYF PLQSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAGI CASYQTQTNS PGSASSVASQ SIIAYTMSLG AENSVAYSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GAALQIPFAM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TASALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DFCGKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVSGNCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK |
-Macromolecule #2: sybody#15
Macromolecule | Name: sybody#15 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: QVQLVESGGG LVQAGGSLRL SCAASGFPVK NFEMEWYRKA PGKEREWVAA IQSGGVETYY ADSVK GRFT ISRDNAKNTV YLQMNSLKPE DTAVYYCFVY VGRSYIGQGT QVTVS |
-Macromolecule #3: sybody#68
Macromolecule | Name: sybody#68 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Sequence | String: QVQLVESGGG SVQAGGSLRL SCAASGSISS ITYLGWFRQA PGKEREGVAA LITVNGHTYY ADSVK GRFT VSLDNAKNTV YLQMNSLKPE DTALYYCAAA AWGYAWPLHQ DDYWYWGQGT QVTVS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 8 / Details: 2 mM Tris-HCl pH 8.0, 200 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: at 15mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 90.0 K / Max: 105.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 5 / Number real images: 12454 / Average exposure time: 9.0 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 49407 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |