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- EMDB-33204: S-ECD (Omicron) in complex with PD of ACE2 focused on RBD_PD sub-... -

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Basic information

Entry
Database: EMDB / ID: EMD-33204
TitleS-ECD (Omicron) in complex with PD of ACE2 focused on RBD_PD sub-complex
Map data
Sample
  • Complex: S-ECD (Omicron) in complex with PD of ACE2
    • Complex: S-ECD (Omicron)
    • Complex: ACE2
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi YN / Shen YP / Zhang YY / Yan RH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169204 China
CitationJournal: iScience / Year: 2022
Title: Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants.
Authors: Yaning Li / Qing Fan / Bing Zhou / Yaping Shen / Yuanyuan Zhang / Lin Cheng / Furong Qi / Shuo Song / Yingying Guo / Renhong Yan / Bin Ju / Zheng Zhang /
Abstract: The different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have attracted most public concern because they caused "wave and wave" COVID-19 pandemic. The initial step of ...The different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have attracted most public concern because they caused "wave and wave" COVID-19 pandemic. The initial step of viral infection is mediated by the SARS-CoV-2 Spike (S) protein, which mediates the receptor recognition and membrane fusion between virus and host cells. Neutralizing antibodies (nAbs) targeting the S protein of SARS-CoV-2 have become promising candidates for clinical intervention strategy, while multiple studies have shown that different variants have enhanced infectivity and antibody resistance. Here, we explore the structure and function of STS165, a broadly inter-Spike bivalent nAb against SARS-CoV-2 variants and even SARS-CoV, contributing to further understanding of the working mechanism of nAbs.
History
DepositionApr 12, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33204.png

Downloads & links

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Map

FileDownload / File: emd_33204.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1325239 - 2.1110537
Average (Standard dev.)0.0072512873 (±0.0475301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33204_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_33204_half_map_2.map
Projections & Slices
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Sample components

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Entire : S-ECD (Omicron) in complex with PD of ACE2

EntireName: S-ECD (Omicron) in complex with PD of ACE2
Components
  • Complex: S-ECD (Omicron) in complex with PD of ACE2
    • Complex: S-ECD (Omicron)
    • Complex: ACE2

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Supramolecule #1: S-ECD (Omicron) in complex with PD of ACE2

SupramoleculeName: S-ECD (Omicron) in complex with PD of ACE2 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: S-ECD (Omicron)

SupramoleculeName: S-ECD (Omicron) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: ACE2

SupramoleculeName: ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 65532
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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