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- EMDB-29471: SARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (two RBD o... -

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Basic information

Entry
Database: EMDB / ID: EMD-29471
TitleSARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (two RBD observed, one RBD scattered)
Map data
Sample
  • Complex: SARS-CoV-2 Spike Protein Variant D614G
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsEgri SB / Wang X / Diaz-Salinas M / Luban J / Dudkina N / Munro J / Shen K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2023
Title: Detergent modulates the conformational equilibrium of SARS-CoV-2 Spike during cryo-EM structural determination.
Authors: Shawn B Egri / Xue Wang / Marco A Díaz-Salinas / Jeremy Luban / Natalya V Dudkina / James B Munro / Kuang Shen /
Abstract: The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD ...The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD has been reported to adopt two primary conformations, a closed conformation in which the binding site is shielded and unable to interact with ACE2, and an open conformation that is capable of binding ACE2. Many structural studies have probed the conformational space of the homotrimeric Spike from SARS-CoV-2. However, how sample buffer conditions used during structural determination influence the Spike conformation is currently unclear. Here, we systematically explored the impact of commonly used detergents on the conformational space of Spike. We show that in the presence of detergent, the Spike glycoprotein predominantly occupies a closed conformational state during cryo-EM structural determination. However, in the absence of detergent, such conformational compaction was neither observed by cryo-EM, nor by single-molecule FRET designed to visualize the movement of RBD in solution in real-time. Our results highlight the highly sensitive nature of the Spike conformational space to buffer composition during cryo-EM structural determination, and emphasize the importance of orthogonal biophysical approaches to validate the structural models obtained.
History
DepositionJan 18, 2023-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateMay 17, 2023-
Current statusMay 17, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29471.png

Downloads & links

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Map

FileDownload / File: emd_29471.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 269.568 Å		1.05 Å/pix.
x 256 pix.
= 269.568 Å		1.05 Å/pix.
x 256 pix.
= 269.568 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.37193435 - 0.8616193
Average (Standard dev.)-0.0025863303 (±0.038205087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 269.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29471_half_map_1.map
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Half map: #2

Fileemd_29471_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 Spike Protein Variant D614G

EntireName: SARS-CoV-2 Spike Protein Variant D614G
Components
  • Complex: SARS-CoV-2 Spike Protein Variant D614G

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Supramolecule #1: SARS-CoV-2 Spike Protein Variant D614G

SupramoleculeName: SARS-CoV-2 Spike Protein Variant D614G / type: complex / ID: 1 / Chimera: Yes / Parent: 0
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

BufferpH: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

21452

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73434
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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