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- EMDB-13891: SARS-CoV-2 Spike in complex with the neutralizing nanobody VHH-F04 -

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Basic information

Entry
Database: EMDB / ID: EMD-13891
TitleSARS-CoV-2 Spike in complex with the neutralizing nanobody VHH-F04
Map data
Sample
  • Complex: HexaPro Spike Protein in complex with nanobody VHH-F04
    • Complex: VHH-F04
    • Complex: HexaPro Spike protein
Keywordscoronavirus / VHH / nanobody / VIRAL PROTEIN
Biological speciesVicugna pacos (alpaca) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.51 Å
AuthorsGuardado-Calvo P / Fernandez I / Rey FA
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Nanobodies against SARS-CoV-2 neutralize variants of concern and explore conformational differences on the Spike protein
Authors: Fernandez I / Buchrieser J
History
DepositionNov 19, 2021-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13891.png

Downloads & links

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Map

FileDownload / File: emd_13891.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å		0.96 Å/pix.
x 400 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.19
Minimum - Maximum-18.725845 - 35.641199999999998
Average (Standard dev.)0.000000000001624 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HexaPro Spike Protein in complex with nanobody VHH-F04

EntireName: HexaPro Spike Protein in complex with nanobody VHH-F04
Components
  • Complex: HexaPro Spike Protein in complex with nanobody VHH-F04
    • Complex: VHH-F04
    • Complex: HexaPro Spike protein

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Supramolecule #1: HexaPro Spike Protein in complex with nanobody VHH-F04

SupramoleculeName: HexaPro Spike Protein in complex with nanobody VHH-F04
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: VHH-F04

SupramoleculeName: VHH-F04 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: HexaPro Spike protein

SupramoleculeName: HexaPro Spike protein / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90562
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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