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- EMDB-24678: SARS-CoV-2 S/S2M11/SNAP1 Global Refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-24678
TitleSARS-CoV-2 S/S2M11/SNAP1 Global Refinement
Map dataSARS-CoV-2 S/S2M11/SNAP1 Global Refinement unsharpened map
Sample
  • Complex: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDang HV / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: Angew Chem Int Ed Engl / Year: 2021
Title: Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection.
Authors: Nataly Kacherovsky / Lucy F Yang / Ha V Dang / Emmeline L Cheng / Ian I Cardle / Alexandra C Walls / Matthew McCallum / Drew L Sellers / Frank DiMaio / Stephen J Salipante / Davide Corti / ...Authors: Nataly Kacherovsky / Lucy F Yang / Ha V Dang / Emmeline L Cheng / Ian I Cardle / Alexandra C Walls / Matthew McCallum / Drew L Sellers / Frank DiMaio / Stephen J Salipante / Davide Corti / David Veesler / Suzie H Pun /
Abstract: The coronavirus disease 2019 (COVID-19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for ...The coronavirus disease 2019 (COVID-19) pandemic has devastated families and disrupted healthcare, economies and societies across the globe. Molecular recognition agents that are specific for distinct viral proteins are critical components for rapid diagnostics and targeted therapeutics. In this work, we demonstrate the selection of novel DNA aptamers that bind to the SARS-CoV-2 spike glycoprotein with high specificity and affinity (<80 nM). Through binding assays and high resolution cryo-EM, we demonstrate that SNAP1 (SARS-CoV-2 spike protein N-terminal domain-binding aptamer 1) binds to the S N-terminal domain. We applied SNAP1 in lateral flow assays (LFAs) and ELISAs to detect UV-inactivated SARS-CoV-2 at concentrations as low as 5×10  copies mL . SNAP1 is therefore a promising molecular tool for SARS-CoV-2 diagnostics.
History
DepositionAug 12, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24678.png

Downloads & links

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Map

FileDownload / File: emd_24678.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 S/S2M11/SNAP1 Global Refinement unsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 400 pix.
= 464. Å		1.16 Å/pix.
x 400 pix.
= 464. Å		1.16 Å/pix.
x 400 pix.
= 464. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.658
Minimum - Maximum-0.6675196 - 2.074809
Average (Standard dev.)0.0005610636 (±0.05468204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24678_msk_1.map
Projections & Slices
AxesZYX

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Additional map: SARS-CoV-2 S/S2M11/S2X333 Global Refinement locally-filtered map

Fileemd_24678_additional_1.map
AnnotationSARS-CoV-2 S/S2M11/S2X333 Global Refinement locally-filtered map
Projections & Slices
AxesZYX

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Histogram

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Half map: SARS-CoV-2 S/S2M11/SNAP1 Global Refinement half map 1

Fileemd_24678_half_map_1.map
AnnotationSARS-CoV-2 S/S2M11/SNAP1 Global Refinement half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SARS-CoV-2 S/S2M11/SNAP1 Global Refinement half map 2

Fileemd_24678_half_map_2.map
AnnotationSARS-CoV-2 S/S2M11/SNAP1 Global Refinement half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1

EntireName: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1
Components
  • Complex: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1

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Supramolecule #1: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1

SupramoleculeName: SARS-CoV-2 S in complex with S2M11 Fab and DNA aptamer SNAP1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 142 KDa

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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

Concentration0.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTris-HClTrisTris-HClTris
150.0 mMNaClSodium chloridesodium chloride
0.1 %octyl-glucoside

Details: TBS pH 8.0, 25mM Tris-HCl, 150mM NaCl and 0.1% octyl-glucoside
GridModel: C-flat-1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41071

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