+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17451 | |||||||||
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Title | SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Antibody / Spike / Complex / 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 / Enterobacteria phage T4 (virus) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Das H / Hallberg BM | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab domains) Authors: Das H / Hallberg BM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17451.map.gz | 295.9 KB | EMDB map data format | |
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Header (meta data) | emd-17451-v30.xml emd-17451.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17451_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_17451.png | 88.5 KB | ||
Filedesc metadata | emd-17451.cif.gz | 6.2 KB | ||
Others | emd_17451_half_map_1.map.gz emd_17451_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17451 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17451 | HTTPS FTP |
-Validation report
Summary document | emd_17451_validation.pdf.gz | 970.1 KB | Display | EMDB validaton report |
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Full document | emd_17451_full_validation.pdf.gz | 969.7 KB | Display | |
Data in XML | emd_17451_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | emd_17451_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17451 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17451 | HTTPS FTP |
-Related structure data
Related structure data | 8p5mMC 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_17451.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17451_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17451_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Spike RBD (two molecules) in complex with two FU2 nanobodies
Entire | Name: Spike RBD (two molecules) in complex with two FU2 nanobodies |
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Components |
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-Supramolecule #1: Spike RBD (two molecules) in complex with two FU2 nanobodies
Supramolecule | Name: Spike RBD (two molecules) in complex with two FU2 nanobodies type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 95.7 KDa |
-Supramolecule #2: SARS-CoV-2 spike (RBD)
Supramolecule | Name: SARS-CoV-2 spike (RBD) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Monoclonal Antibody Mab-23
Supramolecule | Name: Monoclonal Antibody Mab-23 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Enterobacteria phage T4 (virus) |
-Macromolecule #1: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.002676 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPK UniProtKB: Spike glycoprotein |
-Macromolecule #2: Mab-23 (Heavy chain variable domain)
Macromolecule | Name: Mab-23 (Heavy chain variable domain) / 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: 48.500398 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCTASGFTFS NYGFHWVRQA PGKGLEWVTI ISYDGITKHY ADSVKDRFTV SRDNSKTMVY LQMNNLKLD DTAVYYCARD LGTYDDSWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGLVKDYF PEVTSWNSGA L TSGVHTFP ...String: EVQLVESGGG LVQPGGSLRL SCTASGFTFS NYGFHWVRQA PGKGLEWVTI ISYDGITKHY ADSVKDRFTV SRDNSKTMVY LQMNNLKLD DTAVYYCARD LGTYDDSWGQ GVLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGLVKDYF PEVTSWNSGA L TSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKVEPKSCDK THTCPPCPAP ELLGGPSVFL FP PKPKDTL MISRTPEVTC VVVDVSHEDP EVKFNWYVDG VEVHNAKTKP REEQYNSTYR VVSVLTVLHQ DWLNGKEYKC KVS NKALPA PIEKTISKAK GQPREPQVYT LPPSRDETKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY KTTPPVLDSD GSFF LYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK |
-Macromolecule #3: Mab-23 (Light chain variable domain)
Macromolecule | Name: Mab-23 (Light chain variable domain) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.234852 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSA LSASVGDRVT ISCRASQNID GFLAWYQQKP GKAPKLLIYA ASRLQSGIPS RFSGSGSGTD FTLTISSLQP EDFAAYYCQ QVYSAPLTFG GGTKVEFKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSA LSASVGDRVT ISCRASQNID GFLAWYQQKP GKAPKLLIYA ASRLQSGIPS RFSGSGSGTD FTLTISSLQP EDFAAYYCQ QVYSAPLTFG GGTKVEFKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4774 / Average exposure time: 1.5 sec. / Average electron dose: 48.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |