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

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Basic information

Entry
Database: PDB / ID: 9r6t
TitlePrefusion stabilized spike glycoprotein of equine coronavirus.
ComponentsSpike glycoprotein
KeywordsVIRAL PROTEIN / fusion glycoprotein / membrane protein
Function / homologySapienic acid
Function and homology information
Biological speciesEquine coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMelchers, J.M. / Hulswit, R.J.G. / Hurdiss, D.L.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: PLoS Pathog / Year: 2026
Title: AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal embecovirus antigen design.
Authors: Jelle M Melchers / Jarek Juraszek / Ruben J G Hulswit / Daan van Overveld / Lam Le / Frank J M van Kuppeveld / Daniel L Hurdiss / Berend-Jan Bosch / Johannes P M Langedijk / Mark J G Bakkers /
Abstract: The continued threat of zoonotic coronavirus spillovers underscores the need for cross-species applicable vaccine design strategies. The genus Embecovirus includes human coronaviruses OC43 and HKU1 ...The continued threat of zoonotic coronavirus spillovers underscores the need for cross-species applicable vaccine design strategies. The genus Embecovirus includes human coronaviruses OC43 and HKU1 as well as relevant veterinary pathogens. The coronavirus spike (S) fusion glycoprotein, key to viral entry and protective immunity, is inherently metastable, complicating vaccine development. Using the ReCaP AI tool, we stabilized the prefusion conformation of OC43 S through rationally combined amino acid substitutions, resulting in markedly enhanced expression and thermal stability. The substitutions were transferable to equine coronavirus (ECoV) S and HKU1. Cryo-EM structures of stabilized OC43 and ECoV S revealed that stabilization was achieved by arresting the release of the fusion peptide and keeping the S1B receptor binding domain in the 'down' state by improving the complex polar interactions of neighboring S1B domains and the bound free fatty acid at the interprotomer S1B interface. This work provides the first ECoV S structure and a broadly applicable framework for engineering stabilized Embecovirus S antigens.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein
B: Spike glycoprotein
C: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,77145
Polymers430,8943
Non-polymers14,87742
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALASNASNAA15 - 123415 - 1234
d_12NAGNAGNAGNAGAEA1401
d_13NAGNAGNAGNAGDD1
d_14NAGNAGNAGNAGDD2
d_15NAGNAGNAGNAGEE1
d_16NAGNAGNAGNAGEE2
d_17NAGNAGNAGNAGFF1
d_18NAGNAGNAGNAGFF2
d_19NAGNAGNAGNAGGG1
d_110NAGNAGNAGNAGGG2
d_111NAGNAGNAGNAGAFA1402
d_112NAGNAGNAGNAGAGA1403
d_113NAGNAGNAGNAGHH1
d_114NAGNAGNAGNAGHH2
d_115NAGNAGNAGNAGII1
d_116NAGNAGNAGNAGII2
d_117NAGNAGNAGNAGJJ1
d_118NAGNAGNAGNAGJJ2
d_119NAGNAGNAGNAGAHA1404
d_120NAGNAGNAGNAGKK1
d_121NAGNAGNAGNAGKK2
d_122NAGNAGNAGNAGLL1
d_123NAGNAGNAGNAGLL2
d_1248Z98Z98Z98Z9COA1401
d_21VALVALASNASNBB15 - 123415 - 1234
d_22NAGNAGNAGNAGBJA1401
d_23NAGNAGNAGNAGMM1
d_24NAGNAGNAGNAGMM2
d_25NAGNAGNAGNAGNN1
d_26NAGNAGNAGNAGNN2
d_27NAGNAGNAGNAGOO1
d_28NAGNAGNAGNAGOO2
d_29NAGNAGNAGNAGPP1
d_210NAGNAGNAGNAGPP2
d_211NAGNAGNAGNAGBKA1402
d_212NAGNAGNAGNAGBLA1403
d_213NAGNAGNAGNAGQQ1
d_214NAGNAGNAGNAGQQ2
d_215NAGNAGNAGNAGRR1
d_216NAGNAGNAGNAGRR2
d_217NAGNAGNAGNAGSS1
d_218NAGNAGNAGNAGSS2
d_219NAGNAGNAGNAGBMA1404
d_220NAGNAGNAGNAGTT1
d_221NAGNAGNAGNAGTT2
d_222NAGNAGNAGNAGUU1
d_223NAGNAGNAGNAGUU2
d_2248Z98Z98Z98Z9AIA1405
d_31VALVALASNASNCC15 - 123415 - 1234
d_32NAGNAGNAGNAGCPA1402
d_33NAGNAGNAGNAGVV1
d_34NAGNAGNAGNAGVV2
d_35NAGNAGNAGNAGWW1
d_36NAGNAGNAGNAGWW2
d_37NAGNAGNAGNAGXX1
d_38NAGNAGNAGNAGXX2
d_39NAGNAGNAGNAGYY1
d_310NAGNAGNAGNAGYY2
d_311NAGNAGNAGNAGCQA1403
d_312NAGNAGNAGNAGCRA1404
d_313NAGNAGNAGNAGZZ1
d_314NAGNAGNAGNAGZZ2
d_315NAGNAGNAGNAGaAA1
d_316NAGNAGNAGNAGaAA2
d_317NAGNAGNAGNAGbBA1
d_318NAGNAGNAGNAGbBA2
d_319NAGNAGNAGNAGCSA1405
d_320NAGNAGNAGNAGcCA1
d_321NAGNAGNAGNAGcCA2
d_322NAGNAGNAGNAGdDA1
d_323NAGNAGNAGNAGdDA2
d_3248Z98Z98Z98Z9BNA1405

NCS oper:
IDCodeMatrixVector
1given(-0.499713780685, -0.86619057925, -0.000133461026889), (0.866190585638, -0.499713787117, 1.78255828289E-5), (-8.2132667095E-5, -0.000106694995652, 0.999999990935)356.059718322, 95.3421670561, 0.138373810819
2given(-0.500202820006, 0.865908234439, 0.000261510389083), (-0.865908267568, -0.500202830125, -2.98636836533E-5), (0.00010494902714, -0.000241381906741, 0.99999996536)95.3803360794, 356.052141114, 0.128356242962

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Components

#1: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 143631.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine coronavirus / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-8Z9 / Sapienic acid


Mass: 254.408 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Trimeric spike glycoprotein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.435 MDa / Experimental value: YES
Source (natural)Organism: Equine coronavirus / Cellular location: membrane
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293
Buffer solutionpH: 7.4 / Details: 20 mM Tris-HCL, 150 mM NaCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraX1.9model fitting
8ISOLDE1.9model fitting
16PHENIX1.20.1_4487:model refinement
17cryoSPARCinitial Euler assignment
19cryoSPARCfinal Euler assignment
21cryoSPARCclassification
23cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 906875
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 397300 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 6.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001829658
ELECTRON MICROSCOPYf_angle_d0.470240413
ELECTRON MICROSCOPYf_chiral_restr0.04034764
ELECTRON MICROSCOPYf_plane_restr0.00315160
ELECTRON MICROSCOPYf_dihedral_angle_d4.19344395
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints1.19807882896E-12
ens_1d_3AAELECTRON MICROSCOPYNCS constraints1.16060904158E-10

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