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- EMDB-53680: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-53680
TitlePorcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the closed conformation bound to 9-O-Ac-Sia.
Map data
Sample
  • Complex: Spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
Keywordscoronavirus / glycoprotein / 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: 3.1 Å
AuthorsFernandez I / Rey FA
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dipeptidase 1 is a functional receptor for coronavirus PHEV
Authors: Dufloo J / Fernandez I / Rey FA / Sanjuan R
History
DepositionMay 13, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_53680.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.16 Å
Density
Contour LevelBy AUTHOR: 0.0878
Minimum - Maximum-0.20580468 - 0.4865743
Average (Standard dev.)0.0005889917 (±0.020094184)
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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Sample components

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Entire : Spike protein

EntireName: Spike protein
Components
  • Complex: Spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

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Supramolecule #1: Spike protein

SupramoleculeName: Spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 3 / 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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-...

MacromoleculeName: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
type: ligand / ID: 4 / Number of copies: 3 / Formula: 5N6
Molecular weightTheoretical: 351.307 Da
Chemical component information

ChemComp-5N6:
9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid

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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

Concentration0.3 mg/mL
BufferpH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 306 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

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67985
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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