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- EMDB-32675: Cryo-EM structure of SARS-CoV S6P trimer in complex with neutrali... -

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Basic information

Entry
Database: EMDB / ID: EMD-32675
TitleCryo-EM structure of SARS-CoV S6P trimer in complex with neutralizing antibody VacW-209
Map data
Sample
  • Complex: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
    • Complex: VacW-209
    • Complex: SARS-CoV-2
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsZheng Q / Sun H / Ju B / Zhang Z / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2022
Title: Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209.
Authors: Bin Ju / Qingbing Zheng / Huimin Guo / Qing Fan / Tingting Li / Shuo Song / Hui Sun / Senlin Shen / Xinrong Zhou / Wenhui Xue / Lingyan Cui / Bing Zhou / Shaowei Li / Ningshao Xia / Zheng Zhang /
History
DepositionJan 22, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32675.png

Downloads & links

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Map

FileDownload / File: emd_32675.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.49419048 - 0.8445248
Average (Standard dev.)-0.00013365483 (±0.012692911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209

EntireName: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
Components
  • Complex: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
    • Complex: VacW-209
    • Complex: SARS-CoV-2

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Supramolecule #1: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209

SupramoleculeName: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: VacW-209

SupramoleculeName: VacW-209 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: SARS-CoV-2

SupramoleculeName: SARS-CoV-2 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271929
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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