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- EMDB-34498: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in compl... -

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Entry
Database: EMDB / ID: EMD-34498
TitleCryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
Map data
Sample
  • Complex: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
    • Complex: Omicron BA.2.12.1 spike protein
    • Complex: Angiotensin-converting enzyme 2
KeywordsSARS-CoV-2 / Omicron BA.2.12.1 / spike protein / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsZhao ZN / Xie YF / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / ...Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / Yeping Sun / Wei Zhang / Zheng Fan / Xin Zhao / Linhuan Wu / Juncai Ma / Odel Y Li / Guijun Shang / Yan Chai / Kefang Liu / Peiyi Wang / George F Gao / Jianxun Qi /
Abstract: Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly ...Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
History
DepositionOct 16, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34498.png

Downloads & links

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Map

FileDownload / File: emd_34498.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.001730164 - 1.9461075
Average (Standard dev.)0.0005202678 (±0.016511703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34498_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34498_half_map_2.map
Projections & Slices
AxesZYX

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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-2 Omicron BA.2.12.1 spike trimer in compl...

EntireName: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
Components
  • Complex: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
    • Complex: Omicron BA.2.12.1 spike protein
    • Complex: Angiotensin-converting enzyme 2

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Supramolecule #1: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in compl...

SupramoleculeName: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Omicron BA.2.12.1 spike protein

SupramoleculeName: Omicron BA.2.12.1 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Angiotensin-converting enzyme 2

SupramoleculeName: Angiotensin-converting enzyme 2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: PDB ENTRY
PDB model - PDB ID:

7knb

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111387
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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