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- EMDB-67940: The structure of the FIPV-1146 S trimer with mixed D0 conformations -

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Basic information

Entry
Database: EMDB / ID: EMD-67940
TitleThe structure of the FIPV-1146 S trimer with mixed D0 conformations
Map data
Sample
  • Complex: FIPV-1146 S
KeywordsFIPV-1146 / PROTEIN BINDING
Biological speciesFelis catus (domestic cat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsSun JQ / Niu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2026
Title: Structure and receptor recognition of type-II feline infectious peritonitis virus spike glycoprotein.
Authors: Sheng Niu / Yuyang Tian / Linh Nguyen / Chongzhi Bai / Xiaohan Hou / Dan Wang / Ziqian Niu / Zhimin Liu / Jianle Ren / Wentao Li / Qihui Wang / Wen-Xia Tian / Junqing Sun / George Fu Gao /
Abstract: Type-II feline infectious peritonitis virus (FIPV-II) is a lethal alphacoronavirus, whose high homology with the human coronavirus CCoV-HuPn-2018 carries the risk of potential zoonotic FIPV-II ...Type-II feline infectious peritonitis virus (FIPV-II) is a lethal alphacoronavirus, whose high homology with the human coronavirus CCoV-HuPn-2018 carries the risk of potential zoonotic FIPV-II transmission to humans. FIPV-II infects felids using cat aminopeptidase N (cAPN) as its cell-entry receptor, but the molecular details remain unclear. Here, we resolved cryo-electron microscopy (cryo-EM) structures of the spike (S) trimer of a representative FIPV-II strain 79-1146 (FIPV-1146), and of its complex with cAPN. The reconstructions reveal structural transitions of the S protein between the "standing" and "lying" receptor-binding domain (RBD) conformation upon complex formation with cAPN in its open conformation. Structural and mutational analyses revealed that the cAPN residues R378, D751 and R779, as well as the N748-linked glycan are essential for high-affinity RBD engagement. Cross-species analysis demonstrated narrow tropism of FIPV-1146, limited to felids and canids. Introducing the N595K and Q596R substitutions found in transmissible gastroenteritis virus (TGEV) into the FIPV-1146 RBD expands its binding capacity to APNs from pig, bovine, horse and giant panda. These findings provide insights into the entry mechanism and zoonotic constraints of FIPV-II, with potential relevance for antiviral strategies against coronaviruses.
History
DepositionDec 22, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67940.png

Downloads & links

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Map

FileDownload / File: emd_67940.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 480 pix.
= 387.84 Å		0.81 Å/pix.
x 480 pix.
= 387.84 Å		0.81 Å/pix.
x 480 pix.
= 387.84 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0668
Minimum - Maximum-0.3586805 - 1.060451
Average (Standard dev.)-0.0007583952 (±0.0269224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 387.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67940_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67940_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : FIPV-1146 S

EntireName: FIPV-1146 S
Components
  • Complex: FIPV-1146 S

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Supramolecule #1: FIPV-1146 S

SupramoleculeName: FIPV-1146 S / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Felis catus (domestic cat)

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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: OTHER

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Electron microscopy

MicroscopeTFS 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 149514
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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