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- EMDB-67106: Structure of HCoV-229E spike proteins on virions by subtomogram a... -

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Basic information

Entry
Database: EMDB / ID: EMD-67106
TitleStructure of HCoV-229E spike proteins on virions by subtomogram averaging: RBD-closed and S2-loose
Map data
Sample
  • Virus: Human coronavirus 229E
    • Protein or peptide: Spike glycoprotein
KeywordsSpike / HCoV-229E / VIRAL PROTEIN
Biological speciesHuman coronavirus 229E
Methodsubtomogram averaging / cryo EM / Resolution: 10.02 Å
AuthorsPeng C / Liang J / 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
DepositionNov 17, 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_67106.png

Downloads & links

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Map

FileDownload / File: emd_67106.map.gz / Format: CCP4 / Size: 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.)
2.74 Å/pix.
x 128 pix.
= 350.72 Å		2.74 Å/pix.
x 128 pix.
= 350.72 Å		2.74 Å/pix.
x 128 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8
Minimum - Maximum-5.991601 - 7.854447
Average (Standard dev.)0.000000000023586 (±0.8149835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 350.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67106_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_67106_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67106_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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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

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Supramolecule #1: Human coronavirus 229E

SupramoleculeName: Human coronavirus 229E / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus 229E
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

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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: 10.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 2198
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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