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- EMDB-51846: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike pro... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51846
TitlePorcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the open conformation
Map data
Sample
  • Complex: Spike
    • Protein or peptide: PHEV Spike
KeywordsCoronavirus / Spike / Entry / VIRAL PROTEIN
Biological speciesPorcine hemagglutinating encephalomyelitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFernandez I / Rey FA
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Microbiol / Year: 2025
Title: Dipeptidase 1 is a functional receptor for a porcine coronavirus.
Authors: Jérémy Dufloo / Ignacio Fernández / Atousa Arbabian / Ahmed Haouz / Nigel Temperton / Luis G Gimenez-Lirola / Félix A Rey / Rafael Sanjuán /
Abstract: Coronaviruses of the subgenus Embecovirus include several important pathogens, such as the human seasonal coronaviruses HKU1 and OC43, bovine coronavirus and porcine haemagglutinating ...Coronaviruses of the subgenus Embecovirus include several important pathogens, such as the human seasonal coronaviruses HKU1 and OC43, bovine coronavirus and porcine haemagglutinating encephalomyelitis virus (PHEV). While sialic acid is thought to be required for embecovirus entry, protein receptors remain unknown for most of these viruses. Here we show that PHEV does not require sialic acid for entry and instead uses dipeptidase 1 (DPEP1) as a receptor. Cryo-electron microscopy at 3.4-4.4 Å resolution revealed that, unlike other embecoviruses, PHEV displays both open and closed conformations of its spike trimer at steady state. The spike receptor-binding domain (RBD) exhibits extremely high sequence variability across embecoviruses, and we found that DPEP1 usage is specific to PHEV. In contrast, the X-ray structure of the RBD-DPEP1 complex at 2.25 Å showed that the structural elements involved in receptor binding are conserved, highlighting the remarkable versatility of this structural organization in adopting novel receptor specificities.
History
DepositionOct 17, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51846.png

Downloads & links

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Map

FileDownload / File: emd_51846.map.gz / Format: CCP4 / Size: 61 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.)
1.16 Å/pix.
x 252 pix.
= 292.32 Å		1.16 Å/pix.
x 252 pix.
= 292.32 Å		1.16 Å/pix.
x 252 pix.
= 292.32 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0514
Minimum - Maximum-0.15963256 - 0.3580516
Average (Standard dev.)0.00056640443 (±0.016934576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 292.31998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51846_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_51846_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51846_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 : Spike

EntireName: Spike
Components
  • Complex: Spike
    • Protein or peptide: PHEV Spike

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Supramolecule #1: Spike

SupramoleculeName: Spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Trimeric protein obtained by recombinant expression
Source (natural)Organism: Porcine hemagglutinating encephalomyelitis virus

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Macromolecule #1: PHEV Spike

MacromoleculeName: PHEV Spike / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine hemagglutinating encephalomyelitis virus
SequenceString: VLGDLKCNTS SINDVDTGVP SISSEVVDVT NGLGTFYVLD RVYLNTTLLL NGYYPISGAT FRNMALKGTR LLSTLWFKPP FLSPFNDGIF AKVKNSRFFK DGVIYSEFPA ITIGSTFVNT SYSIVVEPHT LLINGNLQGL LQISVCQYTM CEYPHTICHP NLGNQRIELW ...String:
VLGDLKCNTS SINDVDTGVP SISSEVVDVT NGLGTFYVLD RVYLNTTLLL NGYYPISGAT FRNMALKGTR LLSTLWFKPP FLSPFNDGIF AKVKNSRFFK DGVIYSEFPA ITIGSTFVNT SYSIVVEPHT LLINGNLQGL LQISVCQYTM CEYPHTICHP NLGNQRIELW HYDTDVVSCL YRRNFTYDVN ADYLYFHFYQ EGGTFYAYFT DTGFVTKFLF KLYLGTVLSH YYVMPLTCDS ALSLEYWVTP LTTRQFLLAF DQDGVLYHAV DCASDFMSEI MCKTSSITPP TGVYELNGYT VQPVATVYRR IPDLPNCDIE AWLNSKTVSS PLNWERKIFS NCNFNMGRLM SFIQADSFGC NNIDASRLYG MCFGSITIDK FAIPNSRKVD LQVGKSGYLQ SFNYKIDTAV SSCQLYYSLP AANVSVTHYN PSSWNRRYGF NNQSFGSRGL HDAVYSQQCF NTPNTYCPCR TSQCIGGAGT GTCPVGTTVR KCFAAVTNAT KCTCWCQPDP STYKGVNAWT CPQSKVSIQP GQHCPGLGLV EDDCSGNPCT CKPQAFIGWS SETCLQNGRC NIFANFILND VNSGTTCSTD LQQGNTNITT DVCVNYDLYG ITGQGILIEV NATYYNSWQN LLYDSSGNLY GFRDYLSNRT FLIRSCYSGR VSAVFHANSS EPALMFRNLK CSHVFNNTIL RQIQLVNYFD SYLGCVVNAY NNTASAVSTC DLTVGSGYCV DYVTALGSAG SFTTGYRFTN FEPFAVNLVN DSIEPVGGLY EIQIPSEFTI GNLEEFIQTS SPKVTIDCAT FVCGDYAACR QQLAEYGSFC ENINAILIEV NELLDTTQLQ VANSLMNGVT LSTKIKDGIN FNVDDINFSP VLGCLGSECN RASTRSAIED LLFDKVKLSD VGFVQAYNNC TGGAEIRDLI CVQSYNGIKV LPPLLSENQI SGYTLAATAA SLFPPWTAAA GVPFYLNVQY RINGLGVTMD VLSQNQKLIA SAFNNALDAI QEGFDATNSA LVKIQSVVNA NAEALNNLLQ QLSNRFGAIS ASLQEILSRL DALEAKAQID RLINGRLTAL NAYVSQQLSD STLVKFSAAQ AMEKVNECVK SQSSRINFCG NGNHIISLVQ NAPYGLYFIH FSYVPTKYVT AKVSPGLCIA GDIGISPKSG YFINVNNSWM FTGSGYYYPE PITQNNVVMM STCAVNYTKA PDLMLNTSTP NLPDFKEELY QWFKNQSSVA PDLSLDYINV TFLDLQDEMN RLQEAIKVLN GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG SLVPRGSHHH HHHHHSAWSH PQFEKGTGGL NDIFEAQKIE WHE

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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

Concentration0.27 mg/mL
BufferpH: 8 / Details: Tris 10 mM, NaCl 100 mM, pH 8.0
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 240000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25044
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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