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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 / 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
Sapienic acid / Spike glycoprotein
Similarity search - Component
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: To Be Published
Title: AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal Embecovirus antigen design
Authors: Melchers, J.M. / Juraszek, J. / Hulswit, R.J.G. / van Overveld, D. / Le, L. / van Kuppeveld, F. / Hurdiss, D.L. / Bosch, B.J. / Langedijk, J.P.M. / Bakkers, M.J.G.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
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) / References: UniProt: R4WAW7
#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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