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- EMDB-53686: Prefusion stabilized spike glycoprotein of human coronavirus OC43. -

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Basic information

Entry
Database: EMDB / ID: EMD-53686
TitlePrefusion stabilized spike glycoprotein of human coronavirus OC43.
Map data
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, receptor-binding domain, HCoV-OC43-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / 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 speciesHuman coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_53686.png

Downloads & links

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Map

FileDownload / File: emd_53686.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 418. Å		0.84 Å/pix.
x 500 pix.
= 418. Å		0.84 Å/pix.
x 500 pix.
= 418. 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-0.4771221 - 0.7456013
Average (Standard dev.)0.0002870291 (±0.009578841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 418.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53686_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53686_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_53686_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 : 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: Human coronavirus OC43 / Strain: ANZ78834.1 / Location in cell: membrane
Molecular weightTheoretical: 452 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: Human coronavirus OC43
Molecular weightTheoretical: 144.009203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLILLISLP TAFAVIGDLN CTLDPRLKGS FNNRDTGLPS ISTDTVDVTN GLGTYYVLDR VYLNTTLFLN GYYPTSGSTY RNMALKGTD LLSTLWFKPP FLSDFINGIF AKVKNTKVFK DGVMYSEFPA ITIGSTFVNT SYSVVVQPRT INSTQDGVNK L QGLLEVSV ...String:
MFLILLISLP TAFAVIGDLN CTLDPRLKGS FNNRDTGLPS ISTDTVDVTN GLGTYYVLDR VYLNTTLFLN GYYPTSGSTY RNMALKGTD LLSTLWFKPP FLSDFINGIF AKVKNTKVFK DGVMYSEFPA ITIGSTFVNT SYSVVVQPRT INSTQDGVNK L QGLLEVSV CQYNMCEYPH TICHPNLGNH FKELWHLDTG VVSCLYKRNF TYDVNATYLY FHFYQEGGTF YAYFTDTGFV TK FLFNVHL GMALSHYYVM PLTCIRRPKD GFSLEYWVTP LTPRQYLLAF NQDGIIFNAV DCMSDFMSEI KCKTQSIAPP TGV YELNGY TVQPIADVYR RKPDLPNCNI EAWLNDKSVP SPLNWERKTF SNCNFNMSSL MSFIQADSFT CNNIDAAKIY GMCF SSITI DKFAIPNGRK VDLQLGNRGY LQRSNYRIDT TATSCQLYYN LPAANVSVSR FNPSTWNKRF GFIEDSVFVP QPTGV FTNH SVVYAQHCFK APKNFCPCSS CPGKNNGIGT CPAGTNSLTC DNLCTLDPIT LKAPDTYKCP QSKSLVGIGE HCSGLA VKS DYCGNNSCTC QPQAFLGWSA DSCLQGDKCN IFANFILHDV NNGLTCSTDL QKANTEIELG VCVNYDLYGI SGQGIFV EV NATYYNSWQN YLYDSNGNLY GFRDYITNRT FMIHSCYSGR VSAAYHANSS EPALLFRNIK CNYVFNNSLT RQLQPINY S FDSYLGCVVN AYNSTAISVQ TCDLTVGSGY CVDYSKNSRA GGAITTGYRF VNFEPFTVNS VNDSLEPVGG LYEIQIPSE FTIGNMEEFI QTSSPKVTID CAAFVCGDYA ACKLQLVGYG SFCDNIEAIL TEVNELLDTT QLQVANSLMN GVTLSTKLKD GVNFNVDDI NFSPVLGCLG SECSKASSRS AIEDLLFDKV KLSDVGFVEA YNNCTGGAEI RDLICIQSYK GIKVLPPLLS E NQISGYTL AATSAQLFPP WTANAGVPFY LNVQYRINGL GVTMDVLSQN QKLIANAFNN ALHAIQQGFD PTNSALVKIQ AV VNANAEA LNNLLQQLSN RFGAISASLQ EILSRLDPPE AEAQIDKLIN GRLTALNAYV SQRLSDSTLV KFSAAQAMEK VNE CVKSQS SRINFCGNGN HIISLVQNAP YGLYFIHFNY VPTKYVTAKV SPGLCIAGNR GIAPKSGYFV NVNNTWMYTG SGYY YPEPI TENNVVVMST CAVNYTKAPY VMLNTLIPNL SDFKEELDQW FKNQTSVAPD LSLDYINVTF LDLQVEMNRL QEAIK VLNQ SYINLKDKGT YEY

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: 33 / 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

Concentration1.0 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92153
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 model
PDB IDChain

6nzk

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9r6s:
Prefusion stabilized spike glycoprotein of human coronavirus OC43.

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