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Yorodumi- EMDB-32422: CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32422 | |||||||||
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Title | 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: 3.19 Å | |||||||||
Authors | Du S / Xiao JY | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: 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_32422.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-32422-v30.xml emd-32422.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_32422.png | 39.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32422 | HTTPS FTP |
-Validation report
Summary document | emd_32422_validation.pdf.gz | 476.9 KB | Display | EMDB validaton report |
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Full document | emd_32422_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | emd_32422_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_32422_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32422 | HTTPS FTP |
-Related structure data
Related structure data | 7wchMC 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_32422.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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) in complex with SWA9
Entire | Name: S6P(B.1.617.2) in complex with SWA9 |
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Components |
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-Supramolecule #1: S6P(B.1.617.2) in complex with SWA9
Supramolecule | Name: S6P(B.1.617.2) in complex with SWA9 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Surface glycoprotein
Macromolecule | Name: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 142.238312 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY ...String: MFVFLVLLPL VSSQCVNLRT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIHV SGTNGTKRFD NPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI VNNATNVVIK VCEFQFCNDP FLDVYYHKNN KSWMESGVYS S ANNCTFEY VSQPFLMDLE GKQGNFKNLR EFVFKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LL ALHRSYL TPGDSSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIYQTSNFR VQP TESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVI RGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYRYRLFR KSNLKPFERD ISTEIYQAGS KPCNG VEGF NCYFPLQSYG FQPTNGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTESN KKFLPF QQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE HVNNSYECDI PIGAGICASY QTQTNSRGSA SSVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNF SQILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLSST PSALGKLQNV VNQNAQALNT L VKQLSSNF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE QGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWS HPQF EK |
-Macromolecule #2: SWA9H
Macromolecule | Name: SWA9H / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 #3: SWA9L
Macromolecule | Name: SWA9L / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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 |
-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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 324843 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |