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- EMDB-67070: PEDV HNXX S trimer with three D0 down -

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Basic information

Entry
Database: EMDB / ID: EMD-67070
TitlePEDV HNXX S trimer with three D0 down
Map dataDeepEMhancer
Sample
  • Complex: PEDV HNXX S trimer with three D0 down
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsPEDV-S protein / 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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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 epidemic diarrhea virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsLiu J / Wang S / Wang J / Su M / Li Z / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
Other government82341085 China
CitationJournal: To Be Published
Title: Locking Spike Domain 0 Conformation Impairs Fusion and Neutralizes Porcine Epidemic Diarrhea Virus
Authors: Wang S / Liu JB / Wang JJ / Su MZ / Li ZM / Wang ZC / Ma Y / Li Y / Liu BH / Zou JH / Habib G / Xiao SB / Li HY / Li M / Liu YT / He J / Li W / Chen XW / Zhou HB / Xiong XL
History
DepositionNov 13, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67070.png

Downloads & links

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Map

FileDownload / File: emd_67070.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.032830797 - 2.2545607
Average (Standard dev.)0.0019405304 (±0.032889273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67070_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_67070_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 : PEDV HNXX S trimer with three D0 down

EntireName: PEDV HNXX S trimer with three D0 down
Components
  • Complex: PEDV HNXX S trimer with three D0 down
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PEDV HNXX S trimer with three D0 down

SupramoleculeName: PEDV HNXX S trimer with three D0 down / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Porcine epidemic diarrhea 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 epidemic diarrhea virus
Molecular weightTheoretical: 145.118328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKSLNYFWLS LPVLSTLSLP QDVTRCSANT NFRRFFSKFN VQAPAVVVLG GYLPIGENQG VNSTWHCAGQ HPTASGVHGI FVSHIRGGH GFEIGISQEP FDPSGYQLYL HKATNGNTNA TARLRICQFP SIKTLGPTAN NDVTTGRNCL FNKAIPAHMS E HSVVGITW ...String:
MKSLNYFWLS LPVLSTLSLP QDVTRCSANT NFRRFFSKFN VQAPAVVVLG GYLPIGENQG VNSTWHCAGQ HPTASGVHGI FVSHIRGGH GFEIGISQEP FDPSGYQLYL HKATNGNTNA TARLRICQFP SIKTLGPTAN NDVTTGRNCL FNKAIPAHMS E HSVVGITW DNDRVTVFSD KIYYFYFKND WSRVATKCYN SGGCAMQYVY EPTYYMLNVT SAGEDGISYQ PCTANCIGYS AN VFATEPN GHIPEGFSFN NWFLLSNDST LVHGKVVSNQ PLLVNCLLAI PKIYGLGQFF SFNQTIDGVC NGAAAQRAPE ALR FNINDT SVILAEGSIV LHTALGTNLS FVCSNSSDPY LATFATPLGA TQVPYYCFLK VDTYNSTVYK FLAVLPPTVR EIVI TKYGD VYVNGFGYLH LGLLDAVTIN FTGHGTDDDV SGFWTIASTN FVDALIEVQG TAIQRILYCD DPVSQLKCSQ VAFDL DDGF YPISSRNLLS HEQPISFVTL PSFNDHSFVN ITVSASFGDH SGANLIASDT TINGFSSFCV DTRQFTISLF YNVTNS YGY VSNSQDSNCP FTLQSVNDYL SFSKFCVSTS LLASACTIDL LGYPDFGSGV KFTSLYFQFT KGELITGTPK PLQGVTD VS FMTLDVCTKY TIYGFKGEGI ITLTNSSFLA GVYYTSDSGQ LLAFKNVTSG AVYSVTPCSF SEQAAYVDDD IVGVISSL S SSTFNSTREL PGFFYHSNDG SNCTEPVLVY SNIGVCKSGS IGYVPSQSGQ VKIAPMVTGN ISIPTNFSMS IRPEYLQLY NTPVSVDCAT YVCNGNSRCK QLLTQYTAAC KTIESALQLS ARLESVEVNS MLTISEEALQ LATISSFNGD GYNFTNVLGV SVYDPASGR VVQKRSFIED LLFNKVVTNG LGTVDEDYKR CSNGRSVADL VCAQYYSGVM VLPGVVDAEK LHMYSASLIG G MVLGGFTS AAALPFSYAV QARLNYLALQ TDVLQRNQQL LAESFNSAIG NMTSAFESVK EAISQTSKGL NTVAHALTKV QE VVNSQGA ALSQLTVQLQ HNFQAISSSI DDIYSRLDIL SADVQVDRLI TGRLSALNAF VSQTLTKYTE VQASRKLAQQ KVN ECVKSQ SQRYGFCGGD GEHIFSLVQA APQGLLFLHT VLVPGDFVDV IAIAGLCVND EIALTLREPG LVLFTHELQN HTAT EYFVS SRRMFEPRKP TVSDFVQIES CVVTYVNLTR DQLPDVIPDY IDVNKTLDEI LASLPNRTGP SLPLDVFNAT YLNLT GEIA DLEQRSESLR NTTEELQSLI YNINNTLVDL EWLNRVETYI KWP

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 24 / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vv5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 35302
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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