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- EMDB-36735: Dimer of SARS-CoV-2 BA.2 spike and IBT-CoV144(C3 symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-36735
TitleDimer of SARS-CoV-2 BA.2 spike and IBT-CoV144(C3 symmetry)
Map data
Sample
  • Complex: complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144
KeywordsSpike / nanobody / dimer / local / VIRAL PROTEIN
Biological speciesCamelus bactrianus (Bactrian camel)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsYang Y / Zhang CH
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Exploration (Beijing) / Year: 2024
Title: A novel nanobody broadly neutralizes SARS-CoV-2 via induction of spike trimer dimers conformation.
Authors: Yang Yang / Junfang Zhang / Shengnan Zhang / Chenhui Zhang / Chenguang Shen / Shuo Song / Yanqun Wang / Yun Peng / Xiaohua Gong / Jun Dai / Chongwei Xie / Tatyana Aleksandrovna Khrustaleva / ...Authors: Yang Yang / Junfang Zhang / Shengnan Zhang / Chenhui Zhang / Chenguang Shen / Shuo Song / Yanqun Wang / Yun Peng / Xiaohua Gong / Jun Dai / Chongwei Xie / Tatyana Aleksandrovna Khrustaleva / Vladislav Victorovich Khrustalev / Yongting Huo / Di Lu / Da Yao / Jincun Zhao / Yingxia Liu / Hongzhou Lu /
Abstract: The ongoing mutations of the SARS-CoV-2 pose serious challenges to the efficacy of the available antiviral drugs, and new drugs with fantastic efficacy are always deserved investigation. Here, a ...The ongoing mutations of the SARS-CoV-2 pose serious challenges to the efficacy of the available antiviral drugs, and new drugs with fantastic efficacy are always deserved investigation. Here, a nanobody called IBT-CoV144 is reported, which exhibits broad neutralizing activity against SARS-CoV-2 by inducing the conformation of spike trimer dimers. IBT-CoV144 was isolated from an immunized alpaca using the RBD of wild-type SARS-CoV-2, and it showed strong cross-reactive binding and neutralizing potency against diverse SARS-CoV-2 variants, including Omicron subvariants. Moreover, the prophylactically and therapeutically intranasal administration of IBT-CoV144 confers fantastic protective efficacy against the challenge of Omicron BA.1 variant in BALB/c mice model. The structure analysis of the complex between spike (S) protein, conducted using Cryo-EM, revealed a special conformation known as the trimer dimers. This conformation is formed by two trimers, with six RBDs in the "up" state and bound by six VHHs. IBT-CoV144 binds to the lateral region of the RBD on the S protein, facilitating the aggregation of S proteins. This aggregation results in steric hindrance, which disrupts the recognition of the virus by ACE2 on host cells. The discovery of IBT-CoV144 will provide valuable insights for the development of advanced therapeutics and the design of next-generation vaccines.
History
DepositionJul 4, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36735.png

Downloads & links

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Map

FileDownload / File: emd_36735.map.gz / Format: CCP4 / Size: 567.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 530 pix.
= 446.26 Å		0.84 Å/pix.
x 530 pix.
= 446.26 Å		0.84 Å/pix.
x 530 pix.
= 446.26 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0033
Minimum - Maximum-0.014687146 - 0.0367374
Average (Standard dev.)0.000102744045 (±0.0009293743)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin555554
Dimensions530530530
Spacing530530530
CellA=B=C: 446.26 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36735_msk_1.map
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Half map: #1

Fileemd_36735_half_map_1.map
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Histogram (log scale)

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Half map: #2

Fileemd_36735_half_map_2.map
Projections & Slices
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Sample components

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Entire : complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144

EntireName: complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144
Components
  • Complex: complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144

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Supramolecule #1: complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144

SupramoleculeName: complex of RBD domain of SARS-CoV-2 spike protein and IBT-CoV144
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Camelus bactrianus (Bactrian camel)

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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

Concentration1.2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 90786
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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