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- EMDB-72562: The spike protein of HCoV-OC43 obtained from data collected on 10... -

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Basic information

Entry
Database: EMDB / ID: EMD-72562
TitleThe spike protein of HCoV-OC43 obtained from data collected on 100 kV Tundra at 180kX magnification with Falcon C detector
Map data
Sample
  • Organelle or cellular component: The spike protein of HCoV-OC43
    • Protein or peptide: Spike glycoprotein
KeywordsOC43 spike protein / endemic coronavirus spike / viral entry and fusion / 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: 4.06 Å
AuthorsPathirage R / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165947 United States
CitationJournal: To Be Published
Title: Structural Analysis utilizing data from 100 kV TFS Tundra Microscope
Authors: Dutta M / Pathirage R / Acharya P
History
DepositionSep 8, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72562.png

Downloads & links

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Map

FileDownload / File: emd_72562.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å		1.5 Å/pix.
x 256 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-1.2390783 - 1.8721569
Average (Standard dev.)-0.0012721311 (±0.06849535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72562_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_72562_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : The spike protein of HCoV-OC43

EntireName: The spike protein of HCoV-OC43
Components
  • Organelle or cellular component: The spike protein of HCoV-OC43
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: The spike protein of HCoV-OC43

SupramoleculeName: The spike protein of HCoV-OC43 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
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: 149.144547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL LEVSVCQYNM CEYPQTICHP NLGNHRKELW HLDTGVVSCL YKRNFTYDVN ADYLYFHFYQ EGGTFYAYFT DT GVVTKFL FNVYLGMALS HYYVMPLTCN SKLTLEYWVT PLTSRQYLLA FNQDGIIFNA VDCMSDFMSE IKCKTQSIAP PTG VYELNG YTVQPIADVY RRKPNLPNCN IEAWLNDKSV PSPLNWERKT FSNCNFNMSS LMSFIQADSF TCNNIDAAKI YGMC FSSIT IDKFAIPNGR KVDLQLGNLG YLQSFNYRID TTATSCQLYY NLPAANVSVS RFNPSTWNKR FGFIEDSVFK PRPAG VLTN HDVVYAQHCF KAPKNFCPCK LNGSCVGSGP GKNNGIGTCP AGTNYLTCDN LCTPDPITFT GTYKCPQTKS LVGIGE HCS GLAVKSDYCG GNSCTCRPQA FLGWSADSCL QGDKCNIFAN FILHDVNSGL TCSTDLQKAN TDIILGVCVN YDLYGIL GQ GIFVEVNATY YNSWQNLLYD SNGNLYGFRD YITNRTFMIR SCYSGRVSAA FHANSSEPAL LFRNIKCNYV FNNSLTRQ L QPINYFDSYL GCVVNAYNST AISVQTCDLT VGSGYCVDYS KNGGSGGAIT TGYRFTNFEP FTVNSVNDSL EPVGGLYEI QIPSEFTIGN MVEFIQTSSP KVTIDCAAFV CGDYAACKSQ LVEYGSFCDN INAILTEVNE LLDTTQLQVA NSLMNGVTLS TKLKDGVNF NVDDINFSPV LGCLGSECSK ASSRSAIEDL LFDKVKLSDV GFVEAYNNCT GGAEIRDLIC VQSYKGIKVL P PLLSENQF SGYTLAATSA SLFPPWTAAA GVPFYLNVQY RINGLGVTMD VLSQNQKLIA NAFNNALYAI QEGFDATNSA LV KIQAVVN ANAEALNNLL QQLSNRFGAI SASLQEILSR LDALEAEAQI DRLINGRLTA LNAYVSQQLS DSTLVKFSAA QAM EKVNEC VKSQSSRINF CGNGNHIISL VQNAPYGLYF IHFSYVPTKY VTARVSPGLC IAGDRGIAPK SGYFVNVNNT WMYT GSGYY YPEPITENNV VVMSTCAVNY TKAPYVMLNT SIPNLPDFKE ELDQWFKNQT SVAPDLSLDY INVTFLDLGS GYIPE APRD GQAYVRKDGE WVLLSTFLGR SLEVLFQGPG HHHHHHHHSA WSHPQFEKGG GSGGGGSGGS AWSHPQFEK

UniProtKB: Spike glycoprotein

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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

Concentration1.7 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA PLUNGER
Details1.7 milligrams per mili liter of spike was incubate with excess DH1294 Fab in 1:6 molar ratio

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number real images: 7675 / Average electron dose: 31.1 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

DetailsTFS Falcon C Detector
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ohw

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 97429
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot
Output model

PDB-9y6h:
The spike protein of HCoV-OC43 obtained from data collected on 100 kV Tundra at 180kX magnification with Falcon C detector

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