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- EMDB-31819: Negative staining (NS)-EM structure of SARS-CoV-2 S-Delta variant... -

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Basic information

Entry
Database: EMDB / ID: EMD-31819
TitleNegative staining (NS)-EM structure of SARS-CoV-2 S-Delta variant in complex with neutralizing antibodies, RBD-chAb-15 and RBD-chAb45
Map dataNSEM structure of SARS-CoV-2 S-Delta variant in complex with neutralizing antibodies, RBD-chAb-15 and RBD-chAb45
Sample
  • Organelle or cellular component: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 7.0 Å
AuthorsYu PY / Yang TJ / Chang YC / Wu HC / Hsu STD
Funding support Taiwan, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-3114-Y-001-001 Taiwan
Academia Sinica (Taiwan)AS-CDA-109-L08 Taiwan
Academia Sinica (Taiwan)AS-CFII-108-110 Taiwan
Academia Sinica (Taiwan)AS-CFII108-111 Taiwan
CitationJournal: To Be Published
Title: Negative staining (NS)-EM structure of SARS-CoV-2 S-Delta variant in complex with neutralizing antibodies, RBD-chAb-15 and RBD-chAb45
Authors: Yu PY / Yang TJ / Chang YC / Wu HC / Hsu STD
History
DepositionAug 25, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31819.png

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Map

FileDownload / File: emd_31819.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNSEM structure of SARS-CoV-2 S-Delta variant in complex with neutralizing antibodies, RBD-chAb-15 and RBD-chAb45
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.0075698 - 2.0850527
Average (Standard dev.)-0.009624251 (±0.14783946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 435.2 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 spike glycoprotein in complex with neutralizing antibodies

EntireName: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies
Components
  • Organelle or cellular component: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies

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Supramolecule #1: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies

SupramoleculeName: SARS-CoV-2 spike glycoprotein in complex with neutralizing antibodies
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: S-Delta variant, two neutralizing antibodies RBD-chAb-15 and RBD-chAb-45
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightExperimental: 540 KDa
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
50.0 mMTris
150.0 mMNaCl
0.02 %sodium azide
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Startup modelType of model: INSILICO MODEL
Details: generated by ab-initio reconstruction in cryoSparc v2
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4622
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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