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- EMDB-32422: CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-32422
TitleCryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWA9 Fab
Map data
Sample
  • Complex: S6P(B.1.617.2) in complex with SWA9
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: SWA9H
    • Protein or peptide: SWA9L
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsDu S / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionDec 20, 2021-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32422.png

Downloads & links

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Map

FileDownload / File: emd_32422.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.304
Minimum - Maximum-1.4919161 - 3.180181
Average (Standard dev.)-0.00029808527 (±0.06546307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : S6P(B.1.617.2) in complex with SWA9

EntireName: S6P(B.1.617.2) in complex with SWA9
Components
  • Complex: S6P(B.1.617.2) in complex with SWA9
    • Protein or peptide: Surface glycoprotein
    • Protein or peptide: SWA9H
    • Protein or peptide: SWA9L

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Supramolecule #1: S6P(B.1.617.2) in complex with SWA9

SupramoleculeName: S6P(B.1.617.2) in complex with SWA9 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 142.238312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: SWA9H

MacromoleculeName: SWA9H / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.304322 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #3: SWA9L

MacromoleculeName: SWA9L / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.182615 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPVT LSLSPGERAT LSCRASQSVR NSLLAWYQQK PGQAPRLLIY AASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFVVYYC QQHGSSPPWT FGQGTKVEFK RT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 324843

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