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- EMDB-38144: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ... -

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Entry
Database: EMDB / ID: EMD-38144
TitleCryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 2 RBD-up,1 ACE2-binding
Map dataCryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 2 RBD-up,1 ACE2-binding
Sample
  • Complex: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 1-up state
KeywordsSARS-CoV / spike protein / 6P / rabbit ACE2 / 2-up / VIRAL PROTEIN
Biological speciesSARS coronavirus Tor2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.64 Å
AuthorsLi LJ / Shi KY / Yu GH / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: mBio / Year: 2024
Title: Structural basis of increased binding affinities of spikes from SARS-CoV-2 Omicron variants to rabbit and hare ACE2s reveals the expanding host tendency.
Authors: Kaiyuan Shi / Linjie Li / Chunliang Luo / Zepeng Xu / Baihan Huang / Sufang Ma / Kefang Liu / Guanghui Yu / George F Gao /
Abstract: The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered ...The potential host range of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been expanding alongside its evolution during the pandemic, with rabbits and hares being considered important potential hosts, supported by a report of rabbit sero-prevalence in nature. We measured the binding affinities of rabbit and hare angiotensin-converting enzyme 2 (ACE2) with receptor-binding domains (RBDs) from SARS-CoV, SARS-CoV-2, and its variants and found that rabbit and hare ACE2s had broad variant tropism, with significantly enhanced affinities to Omicron BA.4/5 and its subsequent-emerged sub-variants (>10 fold). The structures of rabbit ACE2 complexed with either SARS-CoV-2 prototype (PT) or Omicron BA.4/5 spike (S) proteins were determined, thereby unveiling the importance of rabbit ACE2 Q34 in RBD-interaction and elucidating the molecular basis of the enhanced binding with Omicron BA.4/5 RBD. These results address the highly enhanced risk of rabbits infecting SARS-CoV-2 Omicron sub-variants and the importance of constant surveillance.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has swept the globe and caused immense health and economic damage. SARS-CoV-2 has demonstrated a broad host range, indicating a high risk of interspecies transmission and adaptive mutation. Therefore, constant monitoring for potential hosts is of immense importance. In this study, we found that Omicron BA.4/5 and subsequent-emerged sub-variants exhibited enhanced binding to both rabbit and hare angiotensin-converting enzyme 2 (ACE2), and we elucidated the structural mechanism of their recognition. From the structure, we found that Q34, a unique residue of rabbit ACE2 compared to other ACE2 orthologs, plays an important role in ACE2 recognition. These results address the probability of rabbits/hares being potential hosts of SARS-CoV-2 and broaden our knowledge regarding the molecular mechanism of SARS-CoV-2 interspecies transmission.
History
DepositionNov 27, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38144.png

Downloads & links

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Map

FileDownload / File: emd_38144.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 2 RBD-up,1 ACE2-binding
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å		0.88 Å/pix.
x 520 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.48421973 - 1.3611188
Average (Standard dev.)-0.0010589791 (±0.026445052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of SARS-CoV spike protein(6P) in complex...

Fileemd_38144_half_map_1.map
AnnotationCryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 2 RBD-up,1 ACE2-binding(half A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of SARS-CoV spike protein(6P) in complex...

Fileemd_38144_half_map_2.map
AnnotationCryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 2 RBD-up,1 ACE2-binding(half B)
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 map of SARS-CoV spike protein(6P) in complex with rabbit ...

EntireName: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 1-up state
Components
  • Complex: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 1-up state

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Supramolecule #1: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ...

SupramoleculeName: Cryo-EM map of SARS-CoV spike protein(6P) in complex with rabbit ACE2, 1-up state
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: SARS coronavirus Tor2

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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: 50.0 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: 4.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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