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- EMDB-39209: Cryo-EM structure of SARS-CoV-2 prototype spike protein in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-39209
TitleCryo-EM structure of SARS-CoV-2 prototype spike protein in complex with raccoon dog ACE2
Map data
Sample
  • Complex: SARS-CoV-2 prototype spike in complex with raccoon dog ACE2
KeywordsSARS-CoV-2 prototype / spike / raccoon dog ACE2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsLi LJ / Luo CL / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: PLoS Pathog / Year: 2024
Title: Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Authors: Chunliang Luo / Linjie Li / Yuhang Gu / Hangchuan Zhang / Zepeng Xu / Junqing Sun / Kaiyuan Shi / Sufang Ma / Wen-Xia Tian / Kefang Liu / George F Gao /
Abstract: Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) ...Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) protein receptor binding domain (RBD) of SARS-CoV-2 prototype (PT) and its variants. It revealed that the binding affinities of RBD from SARS-CoV-2 variants were generally lower than that of the PT RBD. Through structural and functional analyses, we found amino acids H34 and M82 play pivotal roles in maintaining the binding affinity of ACE2 to different SARS-CoV-2 sub-variants. These results suggest that raccoon dogs exhibit lower susceptibility to SARS-CoV-2 compared to those animal species with a high prevalence of SARS-CoV-2 transmission.
History
DepositionFeb 23, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39209.png

Downloads & links

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Map

FileDownload / File: emd_39209.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 560 pix.
= 386.4 Å		0.69 Å/pix.
x 560 pix.
= 386.4 Å		0.69 Å/pix.
x 560 pix.
= 386.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.25603536 - 0.90214854
Average (Standard dev.)-0.0003497718 (±0.023187464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39209_msk_1.map
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Half map: #1

Fileemd_39209_half_map_1.map
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Half map: #2

Fileemd_39209_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 prototype spike in complex with raccoon dog ACE2

EntireName: SARS-CoV-2 prototype spike in complex with raccoon dog ACE2
Components
  • Complex: SARS-CoV-2 prototype spike in complex with raccoon dog ACE2

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Supramolecule #1: SARS-CoV-2 prototype spike in complex with raccoon dog ACE2

SupramoleculeName: SARS-CoV-2 prototype spike in complex with raccoon dog ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 309215
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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