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Yorodumi- EMDB-50424: SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50424 | |||||||||
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Title | SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76 (focused refinement) | |||||||||
Map data | sharped map | |||||||||
Sample |
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Keywords | SARS-CoV-2 / Spike / single chain fragment / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information virion component / 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 ...virion component / 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) / Enterobacteria phage T4 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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: Structure of scFv76 in complex with SARS-CoV-2 Omicron Spike protein 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_50424.map.gz | 229.7 MB | EMDB map data format | |
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Header (meta data) | emd-50424-v30.xml emd-50424.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_50424.png | 82 KB | ||
Masks | emd_50424_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-50424.cif.gz | 7.1 KB | ||
Others | emd_50424_additional_1.map.gz emd_50424_half_map_1.map.gz emd_50424_half_map_2.map.gz | 120.6 MB 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50424 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50424 | HTTPS FTP |
-Validation report
Summary document | emd_50424_validation.pdf.gz | 858.7 KB | Display | EMDB validaton report |
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Full document | emd_50424_full_validation.pdf.gz | 858.3 KB | Display | |
Data in XML | emd_50424_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_50424_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50424 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50424 | HTTPS FTP |
-Related structure data
Related structure data | 9fgtMC C: citing same article (ref.) M: atomic model generated by this map |
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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_50424.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharped 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_50424_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharped map
File | emd_50424_additional_1.map | ||||||||||||
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Annotation | unsharped map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50424_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50424_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Spike protein in complex with the single chain fragmen...
Entire | Name: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Spike protein in complex with the single chain fragmen...
Supramolecule | Name: SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 510 KDa |
-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 |
-Supramolecule #3: scFv76 single chain fragment
Supramolecule | Name: scFv76 single chain fragment / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Spike glycoprotein,Fibritin
Macromolecule | Name: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) |
Molecular weight | Theoretical: 135.255156 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISR FDNPVLPFND GVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT F EYVSQPFL ...String: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISR FDNPVLPFND GVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDVYYHK NNKSWMESEF RVYSSANNCT F EYVSQPFL MDLEGKQGNF KNLREFVFKN IDGYFKIYSK HTPIIVPEDL PQGFSALEPL VDLPIGINIT RFQTLLALHR SS SGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TESIVRFPNI TNL CPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNL APFFTFKCYG VSPTKLNDLC FTNVYADSFV IRGDEVRQIA PGQT GNIAD YNYKLPDDFT GCVIAWNSNK LDSKVSGNYN YLYRLFRKSN LKPFERDIST EIYQAGNKPC NGVAGFNCYF PLRSY SFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLKGT GVLTESNKKF LPFQQFGRDI ADTTDA VRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVNVFQTRAG CLIGAEYVNN SYECDIPIGA GICASYQ TS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVDCT MYICGDSTEC SNLLLQYGSF CTQLKRAL T GIAVEQDKNT QEVFAQVKQI YKTPPIKYFG GFNFSQILPD PSKSKRSFIE DLLFNKVTKF KGLTVLPPLL TDEMIAQYT SALLAGTITS GWTFGAGAAL QIPFAMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTASA LGKLQDVVNH NAQALNTLV KQLSSKFGAI SSVLNDIFSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV L GQSKRVDF CGKGYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QI ITTDNTF VSGNCDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLN ESLIDL QELGKYEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGG GSGGS AWSHPQFEK UniProtKB: Spike glycoprotein, Fibritin |
-Macromolecule #2: Single chain fragment scFv76
Macromolecule | Name: Single chain fragment scFv76 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.040947 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RTMEEVQLLQ SAGGLVQPGG SLRLSCAASG FTVSANYMSW VRQAPGKGLE WVSVIYPGGS TFYADSVKGR FTISRDNSKN TLYLQMNSL RVEDTAVYYC ARDLSVAGAF DIWGQGTLVT VSSGGGGSGG GGSGGGGSEI VLTQSPGTLS LSPGERATLS C RASQSVSS ...String: RTMEEVQLLQ SAGGLVQPGG SLRLSCAASG FTVSANYMSW VRQAPGKGLE WVSVIYPGGS TFYADSVKGR FTISRDNSKN TLYLQMNSL RVEDTAVYYC ARDLSVAGAF DIWGQGTLVT VSSGGGGSGG GGSGGGGSEI VLTQSPGTLS LSPGERATLS C RASQSVSS SYLAWYQQKP GQAPRLLIYG ASSRATGIPD RFSGSGSGTD FTLTISRLEP EDFAVYYCQQ YGSSPYTFGQ GT KLEIKRA AAGDYKDDDD KHHHHHH |
-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: 1 / 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 | 0.6 mg/mL |
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Buffer | pH: 7 / Details: PBS |
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: 7179 / 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: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |