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- EMDB-66668: Structure of HCoV-229E spike proteins on virions by subtomogram a... -

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Basic information

Entry
Database: EMDB / ID: EMD-66668
TitleStructure of HCoV-229E spike proteins on virions by subtomogram averaging: RBD-closed and S2-compact
Map data
Sample
  • Virus: Human coronavirus 229E
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSpike / HCoV-229E / 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 / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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 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 229E
Methodsubtomogram averaging / cryo EM / Resolution: 4.55 Å
AuthorsLiang J / Peng C / Li S
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32241031 China
National Natural Science Foundation of China (NSFC)32171195 China
National Natural Science Foundation of China (NSFC)82241066 China
CitationJournal: To Be Published
Title: Cryo-ET analysis of the modulation of the spike protein in alphacoronavirus by temperature and receptor
Authors: Liang J / Peng C / Zhang Z / Song Y / Li S
History
DepositionOct 20, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66668.png

Downloads & links

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Map

FileDownload / File: emd_66668.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.22
Minimum - Maximum-17.497019999999999 - 31.306639000000001
Average (Standard dev.)-0.000000000016114 (±2.2585866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 350.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66668_msk_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_66668_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_66668_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human coronavirus 229E

EntireName: Human coronavirus 229E
Components
  • Virus: Human coronavirus 229E
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human coronavirus 229E

SupramoleculeName: Human coronavirus 229E / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: human cell culture / NCBI-ID: 11137 / Sci species name: Human coronavirus 229E / Sci species strain: ATCC-VR740 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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 229E
Molecular weightTheoretical: 128.755422 KDa
SequenceString: MFVLLVAYAL LHIAGCQTTN GLNTSYSVCN GCVGYSENVF AVESGGYIPS DFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGLR FTTGFVYFNG TGRGDCKGFS SDVLSDVIRY NLNFEENLRR GTILFKTSYG VVVFYCTNNT LVSGDAHIPF G TVLGNFYC ...String:
MFVLLVAYAL LHIAGCQTTN GLNTSYSVCN GCVGYSENVF AVESGGYIPS DFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGLR FTTGFVYFNG TGRGDCKGFS SDVLSDVIRY NLNFEENLRR GTILFKTSYG VVVFYCTNNT LVSGDAHIPF G TVLGNFYC FVNTTIGNET TSAFVGALPK TVREFVISRT GHFYINGYRY FTLGNVEAVN FNVTTAETTD FFTVALASYA DV LVNVSQT SIANIIYCNS VINRLRCDQL SFDVPDGFYS TSPIQSVELP VSIVSLPVYH KHTFIVLYVD FKPQSGGGKC FNC YPAGVN ITLANFNETK GPLCVDTSHF TTKYVAVYAN VGRWSASINT GNCPFSFGKV NNFVKFGSVC FSLKDIPGGC AMPI VANWA YSKYYTIGSL YVSWSDGDGI TGVPQPVEGV SSFMNVTLDK CTKYNIYDVS GVGVIRVSND TFLNGITYTS TSGNL LGFK DVTKGTIYSI TPCNPPDQLV VYQQAVVGAM LSENFTSYGF SNVVELPKFF YASNGTYNCT DAVLTYSSFG VCADGS IIA VQPRNVSYDS VSAIVTANLS IPSNWTTSVQ VEYLQITSTP IVVDCSTYVC NGNVRCVELL KQYTSACKTI EDALRNS AR LESADVSEML TFDKKAFTLA NVSSFGDYNL SSVIPSLPTS GSRVAGRSAI EDILFSKLVT SGLGTVDADY KNCTKGLS I ADLACAQYYN GIMVLPGVAD AERMAMYTGS LIGGIALGGL TSAVSIPFSL AIQARLNYVA LQTDVLQENQ KILAASFNK AMTNIVDAFT GVNDAITQTS QALQTVATAL NKIQDVVNQQ GNSLNHLTSQ LRQNFQAISS SIQAIYDRLD TIQADQQVDR LITGRLAAL NVFVSHTLTK YTEVRASRQL AQQKVNECVK SQSKRYGFCG NGTHIFSIVN AAPEGLVFLH TVLLPTQYKD V EAWSGLCV DGTNGYVLRQ PNLALYKEGN YYRITSRIMF EPRIPTMADF VQIENCNVTF VNISRSELQT IVPEYIDVNK TL QELSYKL PNYTVPDLVV EQYNQTILNL TSEISTLENK SAELNYTVQK LQTLIDNINS TLVDLKWLNR VETYIKWPWW VWL CISVVL IFVVSMLLLC CCSTGCCGFF SCFASSIRGC CESTKLPYYD VEKIHIQ

UniProtKB: Spike glycoprotein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 69 / 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 15058
ExtractionNumber tomograms: 158 / Number images used: 23181 / Software - Name: RELION (ver. 4)
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: predicted by CryoNet
Output model

PDB-9x9j:
Structure of HCoV-229E spike proteins on virions by subtomogram averaging: RBD-closed and S2-compact

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