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- EMDB-53687: Prefusion stabilized spike glycoprotein of equine coronavirus. -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53687
TitlePrefusion stabilized spike glycoprotein of equine coronavirus.
Map dataEM map of the equine coronavirus spike glycoprotein.
Sample
  • Complex: Trimeric spike glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Sapienic acid
Keywordsfusion glycoprotein / membrane 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / 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 glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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 speciesEquine coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMelchers JM / Hulswit RJG / Hurdiss DL
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: To Be Published
Title: AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal Embecovirus antigen design
Authors: Melchers JM / Juraszek J / Hulswit RJG / van Overveld D / Le L / van Kuppeveld F / Hurdiss DL / Bosch BJ / Langedijk JPM / Bakkers MJG
History
DepositionMay 13, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53687.png

Downloads & links

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Map

FileDownload / File: emd_53687.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of the equine coronavirus spike glycoprotein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å		0.84 Å/pix.
x 360 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.73191214 - 0.97892576
Average (Standard dev.)0.0006376272 (±0.021337064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of equine coronavirus spike glycoprotein.

Fileemd_53687_half_map_1.map
AnnotationHalf map of equine coronavirus spike glycoprotein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of equine coronavirus spike glycoprotein.

Fileemd_53687_half_map_2.map
AnnotationHalf map of equine coronavirus spike glycoprotein.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric spike glycoprotein

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

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Supramolecule #1: Trimeric spike glycoprotein

SupramoleculeName: Trimeric spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Equine coronavirus / Location in cell: membrane
Molecular weightTheoretical: 435 KDa

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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: Equine coronavirus
Molecular weightTheoretical: 143.631375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLLLLFFLP TAFAVVGDVK CTTIGVNDVN TGAPVISTET VDVTNGLGTY YVLDRVYLNT TLLLNGYYPT SGANYRNLAL KASELLSTL WYKPPFLSEF NDGVFAKVKN TKVTKNGIVY SEFPTMVIGT TFVNTSYTVV VQPRTTVVNS KLQGLLEITI C QYSMCEYP ...String:
MVLLLLFFLP TAFAVVGDVK CTTIGVNDVN TGAPVISTET VDVTNGLGTY YVLDRVYLNT TLLLNGYYPT SGANYRNLAL KASELLSTL WYKPPFLSEF NDGVFAKVKN TKVTKNGIVY SEFPTMVIGT TFVNTSYTVV VQPRTTVVNS KLQGLLEITI C QYSMCEYP NTVCNSGIGS PRKELWHYEK AVASCLYRRN FTYDVNSDWL YFHFYQQGGT FYAYYTDSGF ITTFLFNIYL GT SLSHYYV MPLSCSGKLD LQYWVTPLTN RQFLLVFNQD GIIYNAVDCA SDYMSEIKCK TQNVKPSTGV YDLTGYTVQP IAD VYRRIP NLPDCNMEDW LSAPTVASPL NWERRTFSNC NFNMSSLLSF IQADSFSCSN IDAAKLYGMC FGSVTIDKFA IPNS RKVDL QLGNRGYLQR FNYRIDTTAT SCQLYYSLGA DNVTVTRSNP SAWNRRYGFN DTMFKPQPAG FFTNHDVVYS KQCFK VPNT YCPCKNNGAT CVGNGVSAGV SGTTTGSGTC PVGTSYRTCF NPIQCACTCD PEPINAILTS GPRACPQVKS LVGLGE HCS GLGIHEDFCG GSPCSCPANA FMAWSVDSCL QDGRCNIFSN LILNGVNSGA TCSTDLQRSN TEIVVGVCVK YDLYGIT GQ GIFIEVNATY YNSWQNLLYD SNGNLYGFRD YLTNRTFMIR SCYSGRVSAA YHSDASEPAL LYRNLKCNYV FNNTIARE G NPINYFDSYL GCIVNADNST SSVVDTCVLT MGSGYCVDYS TASRAGGSPS TGYRLTNFEP FNVRLVNDSV EPVGGLYEI QIPSEFTIGN FEEFIQTNSP KVTIDCAAFV CGDYAACREQ LVGYGSFCDN IEAILTEVND LLDTTQFQVA NSLMNGVTLS SRLKTGINF NVDDINFSSV LGCVGSDCNT VSSRSAIEDL LFNKVRLSDV GFVEAYNNCT GGAEIRDLLC VQTFNGIKVL P PVLSENQI SGYTLAATSA QLFPPWTAAA GIPFYLNVQY RINGLGVTMD VLSQNQKMIA NAFNNALGAI QNGFDPTNSA LV KIQAVVN ANAEALNNLL QQLSNRFGAI SSSLQEILSR LDPPEAQAQI DKLINGRLTA LNAFVSQQLS DTTLVKFSAS QAI EKVNEC VKSQSLRVNF CGNGNHIISL VQNAPYGLYF IHFNYVPTKY VTAKVSPGLC IAGDRGIAPK SGYFVNVNNM WMFT GSGYY YPEPITENNV VVMSTCAVNY TKAPDVMLNI LIPNLSDFKE ELDQWFKNQT SVAPDLSLDY INVTFLNLQD EMNRL QESI KVLNQSYINL KDKGTYEY

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: 12 / 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: Sapienic acid

MacromoleculeName: Sapienic acid / type: ligand / ID: 4 / Number of copies: 3 / Formula: 8Z9
Molecular weightTheoretical: 254.408 Da
Chemical component information

ChemComp-8Z9:
Sapienic 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

Concentration1.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl

Details: 20 mM Tris-HCL, 150 mM NaCl, pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 906875
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 397300
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementProtocol: OTHER
Output model

PDB-9r6t:
Prefusion stabilized spike glycoprotein of equine coronavirus.

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