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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: To Be Published
Title: DPEP1 is the cell receptor of the Porcine Hemagglutinanting Encephalomyelitis Virus
Authors: Dufloo J / Fernandez I / Rey FA / Sanjuan R
History
DepositionOct 17, 2024-
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

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
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51846_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51846_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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