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- EMDB-35986: Cryo-EM structure of SARS-CoV-1 2p spike protein in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-35986
TitleCryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Map dataCryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Sample
  • Complex: Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG
    • Complex: Severe acute respiratory syndrome coronavirus 1-2p
      • Complex: W328-6H2 IgG
KeywordsCryo-EM / Complex / SARS-CoV-1 / antibody / Homo sapiens / IgG / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 6.91 Å
AuthorsNan XY / Li YJ
Funding support1 items
OrganizationGrant numberCountry
Other government22277017
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Authors: Nan XY / Li YJ
History
DepositionApr 22, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35986.png

Downloads & links

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Map

FileDownload / File: emd_35986.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 600 pix.
= 582. Å		0.97 Å/pix.
x 600 pix.
= 582. Å		0.97 Å/pix.
x 600 pix.
= 582. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.33855736 - 1.0146756
Average (Standard dev.)-0.00030147098 (±0.03371458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 582.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of SARS-CoV-1 2p spike protein in...

Fileemd_35986_half_map_1.map
AnnotationCryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of SARS-CoV-1 2p spike protein in...

Fileemd_35986_half_map_2.map
AnnotationCryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG

EntireName: Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG
Components
  • Complex: Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG
    • Complex: Severe acute respiratory syndrome coronavirus 1-2p
      • Complex: W328-6H2 IgG

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Supramolecule #1: Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG

SupramoleculeName: Cryo-EM structure of SARS-CoV-1 2p in complex with W328-6H2 IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Cryo-EM structure of SARS-CoV-1 2p spike protein in complex with W328-6H2 IgG
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 1-2p

SupramoleculeName: Severe acute respiratory syndrome coronavirus 1-2p / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: SARS-CoV-1 2p
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Supramolecule #3: W328-6H2 IgG

SupramoleculeName: W328-6H2 IgG / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #3 / Details: W328-6H2 IgG
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2567 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 148965
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53380
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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