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- EMDB-44658: HCoV-OC43 Spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-44658
TitleHCoV-OC43 Spike glycoprotein
Map dataSharpened map of apo HCoV-OC43 S glycoprotein
Sample
  • Complex: HCoV-OC43 Spike Protein with the introduction two stabilizing Prolines (2P) at residues 1079 and 1080
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHCoV / cryoEM / microfluidics / 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 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-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 speciesHuman coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTorrents de la Pena A / Sewall LM / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136621 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
History
DepositionApr 30, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44658.png

Downloads & links

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Map

FileDownload / File: emd_44658.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of apo HCoV-OC43 S glycoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.53419757 - 0.7998783
Average (Standard dev.)-0.00018728466 (±0.022321628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44658_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map of apo HCoV-OC43 S glycoprotein

Fileemd_44658_additional_1.map
Annotationmap of apo HCoV-OC43 S glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of apo HCoV-OC43 S glycoprotein

Fileemd_44658_half_map_1.map
AnnotationHalf map of apo HCoV-OC43 S glycoprotein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of apo HCoV-OC43 S glycoprotein

Fileemd_44658_half_map_2.map
AnnotationHalf map of apo HCoV-OC43 S 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 : HCoV-OC43 Spike Protein with the introduction two stabilizing Pro...

EntireName: HCoV-OC43 Spike Protein with the introduction two stabilizing Prolines (2P) at residues 1079 and 1080
Components
  • Complex: HCoV-OC43 Spike Protein with the introduction two stabilizing Prolines (2P) at residues 1079 and 1080
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCoV-OC43 Spike Protein with the introduction two stabilizing Pro...

SupramoleculeName: HCoV-OC43 Spike Protein with the introduction two stabilizing Prolines (2P) at residues 1079 and 1080
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus OC43

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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: 151.600172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFLILLISLP TAFAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ DGVNKLQGLL E VSVCQYNM ...String:
MFLILLISLP TAFAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMAL KGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ DGVNKLQGLL E VSVCQYNM CEYPQTICHP NLGNHRKELW HLDTGVVSCL YKRNFTYDVN ADYLYFHFYQ EGGTFYAYFT DTGVVTKFLF NV YLGMALS HYYVMPLTCN SKLTLEYWVT PLTSRQYLLA FNQDGIIFNA VDCMSDFMSE IKCKTQSIAP PTGVYELNGY TVQ PIADVY RRKPNLPNCN IEAWLNDKSV PSPLNWERKT FSNCNFNMSS LMSFIQADSF TCNNIDAAKI YGMCFSSITI DKFA IPNGR KVDLQLGNLG YLQSFNYRID TTATSCQLYY NLPAANVSVS RFNPSTWNKR FGFIEDSVFK PRPAGVLTNH DVVYA QHCF KAPKNFCPCK LNSSLCVGSG PGKNNGIGTC PAGTNYLTCH NLCTPDPITF TGTYKCPQTK SLVGIGEHCS GLAVKS DYC GGNSCTCRPQ AFLGWSADSC LQGDKCNIFA NFILHDVNSG LTCSTDLQKA NTDIILGVCV NYDLYGILGQ GIFVEVN AT YYNSWQNLLY DSNGNLYGFR DYITNRTFMI RSCYSGRVSA AFHANSSEPA LLFRNIKCNY V(UNK)FNNSLTRQ LQPI NYFDS YLGCVVNAYN STAISVQTCD LTVGSGYCVD YSKNRRSRRA ITTGYRFTNF EPFTVNSVND SLEPVGGLYE IQIPS EFTI GNMVEFIQTS SPKVTIDCAA FVCGDYAACK SQLVEYGSFC DNINAILTEV NELLDTTQLQ VANSLMNGVT LSTKLK DGV NFNVDDINFS PVLGCLGSEC SKASSRSAIE DLLFDKVKLS DVGFVEAYNN CTGGAEIRDL ICVQSYKGIK VLPPLLS EN QFSGYTLAAT SASLFPPWTA AAGVPFYLNV QYRINGLGVT MDVLSQNQKL IANAFNNALY AIQEGFDATN SALVKIQA V VNANAEALNN LLQQLSNRFG AISASLQEIL SRLDALEAEA QIDRLINGRL TALNAYVSQQ LSDSTLVKFS AAQAMEKVN ECVKSQSSRI NFCGNGNHII SLVQNAPYGL YFIHFSYVPT KYVTARVSPG LCIAGDRGIA PKSGYFVNVN NTWMYTGSGY YYPEPITEN NVVVMSTCAV NYTKAPYVML NTSTPNLPDF REELDQWFKN QTSVAPDLSL DYINVTFLDL QVEMNRLQEA I KVLNQSYI NLKDIGTYEY YVKWPWYVWL LIGLAGVAML VLLFFICCCT GCGTSCFKKC GGCCDDYTGY QELVIKTSHD DH HHHHHHH

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: 30 / 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

Concentration0.02 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: EMS Lacey Carbon / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Details: no pretreatment
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: graphene oxide grids, 2.5s blot time, 30s blot time, double blotted, blot force 1.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number real images: 839 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000

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Image processing

Particle selectionNumber selected: 164473
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18599
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 14000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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