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- EMDB-32429: Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-32429
TitleLocal CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
Map data
Sample
  • Complex: the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
    • Protein or peptide: SWC11H
    • Protein or peptide: SWC11L
    • Protein or peptide: Surface glycoprotein
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsDu S / Xiao JY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Local CryoEM structure of the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 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_32429.png

Downloads & links

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Map

FileDownload / File: emd_32429.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-4.851087 - 8.819826
Average (Standard dev.)-0.000490614 (±0.038426794)
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 : the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab

EntireName: the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
Components
  • Complex: the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
    • Protein or peptide: SWC11H
    • Protein or peptide: SWC11L
    • Protein or peptide: Surface glycoprotein

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Supramolecule #1: the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab

SupramoleculeName: the SARS-CoV-2 S6P(B.1.617.2) in complex with SWC11 Fab
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SWC11H

MacromoleculeName: SWC11H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.802607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LIQPGGSLRL SCAASEFIVS RNYMSWVRQA PGTGLEWVSV IYPGGSTFYA DSVKGRFTIS RDNSKNTLYL QMDSLRVED TAVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
EVQLVESGGG LIQPGGSLRL SCAASEFIVS RNYMSWVRQA PGTGLEWVSV IYPGGSTFYA DSVKGRFTIS RDNSKNTLYL QMDSLRVED TAVYYCARDY GDFYFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDK

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Macromolecule #2: SWC11L

MacromoleculeName: SWC11L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.7661 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPVS LSVSPGERAT LSCRASQGVA SNLAWYQQKA GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISTLQS EDSAVYYCQ QYNDRPRTFG QGTKLEIKRT

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Macromolecule #3: Surface glycoprotein

MacromoleculeName: Surface glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.39215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 398316
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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