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Yorodumi- EMDB-32423: Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32423 | |||||||||
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Title | Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | : Function and homology information | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Du S / Xiao JY | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab Authors: Du S / Xiao JY | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32423.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-32423-v30.xml emd-32423.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_32423.png | 39.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32423 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32423 | HTTPS FTP |
-Related structure data
Related structure data | 7wckMC 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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-Map
File | Download / File: emd_32423.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : S6P(B.1.617.2) RBD in complex with SWA9 Fab
Entire | Name: S6P(B.1.617.2) RBD in complex with SWA9 Fab |
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Components |
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-Supramolecule #1: S6P(B.1.617.2) RBD in complex with SWA9 Fab
Supramolecule | Name: S6P(B.1.617.2) RBD in complex with SWA9 Fab / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SWA9H
Macromolecule | Name: SWA9H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.304322 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT NSAMQWVRQA RGQRLEWVGW IVVASGNANS ARRFHDRVTI TSDMSTSTAY LELSSLRSE DTAVYYCALN HCSNTTCLDG FDIWGQGTMV SVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: QMQLVQSGPE VKKPGTSVKV SCKASGFTFT NSAMQWVRQA RGQRLEWVGW IVVASGNANS ARRFHDRVTI TSDMSTSTAY LELSSLRSE DTAVYYCALN HCSNTTCLDG FDIWGQGTMV SVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK |
-Macromolecule #2: SWA9L
Macromolecule | Name: SWA9L / 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: 12.182615 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPVT LSLSPGERAT LSCRASQSVR NSLLAWYQQK PGQAPRLLIY AASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFVVYYC QQHGSSPPWT FGQGTKVEFK RT |
-Macromolecule #3: Surface glycoprotein
Macromolecule | Name: Surface glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.39215 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY RYRLFRKSNL KPFERDISTE IYQAGSKPCN GVEGFNCYFP L QSYGFQPT ...String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY RYRLFRKSNL KPFERDISTE IYQAGSKPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 324843 |