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- EMDB-53679: Local refinement of the N-terminal domain (NTD) and receptor bind... -

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Basic information

Entry
Database: EMDB / ID: EMD-53679
TitleLocal refinement of the N-terminal domain (NTD) and receptor binding domain (RBD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the closed conformation
Map data
Sample
  • Complex: Spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCoronavirus / Spike / Entry / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HEV / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, HEV / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesPorcine hemagglutinating encephalomyelitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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
DepositionMay 13, 2025-
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_53679.png

Downloads & links

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Map

FileDownload / File: emd_53679.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0675
Minimum - Maximum-0.11664796 - 0.31360662
Average (Standard dev.)-0.001173947 (±0.006528896)
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_53679_msk_1.map
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Additional map: Map sharpened with DeepEMhancer

Fileemd_53679_additional_1.map
AnnotationMap sharpened with DeepEMhancer
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Half map: #1

Fileemd_53679_half_map_1.map
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Half map: #2

Fileemd_53679_half_map_2.map
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Sample components

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Entire : Spike

EntireName: Spike
Components
  • Complex: Spike
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Spike

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

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porcine hemagglutinating encephalomyelitis virus
Molecular weightTheoretical: 147.88475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VLGDLKCNTS SINDVDTGVP SISSEVVDVT NGLGTFYVLD RVYLNTTLLL NGYYPISGAT FRNMALKGTR LLSTLWFKPP FLSPFNDGI FAKVKNSRFF KDGVIYSEFP AITIGSTFVN TSYSIVVEPH TLLINGNLQG LLQISVCQYT MCEYPHTICH P NLGNQRIE ...String:
VLGDLKCNTS SINDVDTGVP SISSEVVDVT NGLGTFYVLD RVYLNTTLLL NGYYPISGAT FRNMALKGTR LLSTLWFKPP FLSPFNDGI FAKVKNSRFF KDGVIYSEFP AITIGSTFVN TSYSIVVEPH TLLINGNLQG LLQISVCQYT MCEYPHTICH P NLGNQRIE LWHYDTDVVS CLYRRNFTYD VNADYLYFHF YQEGGTFYAY FTDTGFVTKF LFKLYLGTVL SHYYVMPLTC DS ALSLEYW VTPLTTRQFL LAFDQDGVLY HAVDCASDFM SEIMCKTSSI TPPTGVYELN GYTVQPVATV YRRIPDLPNC DIE AWLNSK TVSSPLNWER KIFSNCNFNM GRLMSFIQAD SFGCNNIDAS RLYGMCFGSI TIDKFAIPNS RKVDLQVGKS GYLQ SFNYK IDTAVSSCQL YYSLPAANVS VTHYNPSSWN RRYGFNNQSF GSRGLHDAVY SQQCFNTPNT YCPCRTSQCI GGAGT GTCP VGTTVRKCFA AVTNATKCTC WCQPDPSTYK GVNAWTCPQS KVSIQPGQHC PGLGLVEDDC SGNPCTCKPQ AFIGWS SET CLQNGRCNIF ANFILNDVNS GTTCSTDLQQ GNTNITTDVC VNYDLYGITG QGILIEVNAT YYNSWQNLLY DSSGNLY GF RDYLSNRTFL IRSCYSGRVS AVFHANSSEP ALMFRNLKCS HVFNNTILRQ IQLVNYFDSY LGCVVNAYNN TASAVSTC D LTVGSGYCVD YVTALRSRRS FTTGYRFTNF EPFAVNLVND SIEPVGGLYE IQIPSEFTIG NLEEFIQTSS PKVTIDCAT FVCGDYAACR QQLAEYGSFC ENINAILIEV NELLDTTQLQ VANSLMNGVT LSTKIKDGIN FNVDDINFSP VLGCLGSECN RASTRSAIE DLLFDKVKLS DVGFVQAYNN CTGGAEIRDL ICVQSYNGIK VLPPLLSENQ ISGYTLAATA ASLFPPWTAA A GVPFYLNV QYRINGLGVT MDVLSQNQKL IASAFNNALD AIQEGFDATN SALVKIQSVV NANAEALNNL LQQLSNRFGA IS ASLQEIL SRLDALEAKA QIDRLINGRL TALNAYVSQQ LSDSTLVKFS AAQAMEKVNE CVKSQSSRIN FCGNGNHIIS LVQ NAPYGL YFIHFSYVPT KYVTAKVSPG LCIAGDIGIS PKSGYFINVN NSWMFTGSGY YYPEPITQNN VVMMSTCAVN YTKA PDLML NTSTPNLPDF KEELYQWFKN QSSVAPDLSL DYINVTFLDL QDEMNRLQEA IKVLNGSGYI PEAPRDGQAY VRKDG EWVL LSTFLGSLVP RGSHHHHHHH HSAWSHPQFE KGTGGLNDIF EAQKIEWHE

UniProtKB: Spike glycoprotein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Details: Tris 10 mM, NaCl 100 mM, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160524
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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