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Yorodumi- EMDB-50417: SARS-CoV-2 (wuhan variant) Spike protein in complex with the sing... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50417 | |||||||||
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Title | SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 | |||||||||
Map data | unsharpened map | |||||||||
Sample |
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Keywords | sars-cov-2 / spike / scfv / single chain fragment / virus / 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 / membrane fusion / 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 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Berlinguer M / Chaves-Sanjuan A / Milazzo FM / Minenkova O / De Santis R / Bolognesi M | |||||||||
Funding support | Italy, 1 items
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Citation | Journal: To Be Published Title: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76-77 Authors: Chaves-Sanjuan A / Bolognesi M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50417.map.gz | 121.5 MB | EMDB map data format | |
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Header (meta data) | emd-50417-v30.xml emd-50417.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_50417.png | 64.7 KB | ||
Masks | emd_50417_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-50417.cif.gz | 5.8 KB | ||
Others | emd_50417_additional_1.map.gz emd_50417_half_map_1.map.gz emd_50417_half_map_2.map.gz | 230.3 MB 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50417 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50417 | HTTPS FTP |
-Validation report
Summary document | emd_50417_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_50417_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_50417_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_50417_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50417 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50417 | HTTPS FTP |
-Related structure data
Related structure data | |
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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_50417.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.889 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50417_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharpened map
File | emd_50417_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50417_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50417_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike protein trimer in complex with the single chain ...
Entire | Name: SARS-CoV-2 Spike protein trimer in complex with the single chain fragment scFv76 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike protein trimer in complex with the single chain ...
Supramolecule | Name: SARS-CoV-2 Spike protein trimer in complex with the single chain fragment scFv76 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 510 KDa |
-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 KPSKRSPIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQKFNGLTV LPPLLTDEMI AQYTSALLAG TITSGWTFGA GPALQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TPSALGKLQD 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 UniProtKB: Spike glycoprotein |
-Macromolecule #2: scFv76-77 single chain fragment
Macromolecule | Name: scFv76-77 single chain fragment / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ...String: RTMEEVQLLQ SAGGLVQPG G SLRLSCAA SG FTVSANY MSW VRQAPG KGLE WVSVI YPGGS TFYA DSVKGR FTI SKDNSKN TL YLQMNSLR V EDTAVYYCA RDLSVAGAFD IWGQGTLVT V SSGGGGSG GG GSGGGGS EIV LTQSPG TLSL SPGEK ATLFC RASQ TFSSNY LAW YQQKPGQ AP SLLIYGGS T RAAGIPDRF SGSGSGTDFT LTINRLEPE D FAIYYCQE YG SSPRVTF GQG TRLEIK RAAA GDYKD DDDKH HHHH H |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3012 / Average electron dose: 40.0 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: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |