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- EMDB-66628: Structure of the HCoV-229E spike glycoprotein determined by subto... -

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Basic information

Entry
Database: EMDB / ID: EMD-66628
TitleStructure of the HCoV-229E spike glycoprotein determined by subtomogram averaging
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: 3.9 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)82241066 China
National Natural Science Foundation of China (NSFC)32171195 China
CitationJournal: Nat Commun / Year: 2026
Title: FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.
Authors: Zheyuan Zhang / Cheng Peng / Weiping Zhang / Jiaming Liang / Kexin Liu / Yong Chen / Junxia Zhang / Rui Liang / Yutong Song / Sai Li /
Abstract: Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the ...Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the labor-intensive, expertise-dependent data processing workflow. Here we present FlyTomo, a software that streamlines data processing from frame alignment to STA with high-throughput for authentic cryo-ET scenarios. During data acquisition, FlyTomo performs real-time diagnosis, enabling prompt feedback on sample quality, microscope performance and structural features. After acquisition, it aggregates diagnostic metrics into an overview, guiding users through data review and refinement. FlyTomo also curates raw and processed data into directories to simplify data management and archiving. We validate FlyTomo across a diverse set of authentic cryo-ET samples, including purified enveloped viruses and cryo-lamellae, on multiple microscopes and cameras, achieving structures at resolutions of 3.4 to 7.3 Å. Collectively, by integrating accuracy, scalability and usability, FlyTomo reduces the technical barrier for in situ structural biology using cryo-ET.
History
DepositionOct 16, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66628.png

Downloads & links

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Map

FileDownload / File: emd_66628.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 257.808 Å		1.07 Å/pix.
x 240 pix.
= 257.808 Å		1.07 Å/pix.
x 240 pix.
= 257.808 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.47
Minimum - Maximum-1.077743 - 2.0369475
Average (Standard dev.)-0.000000000001033 (±0.1376594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 257.808 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66628_msk_1.map
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Half map: #2

Fileemd_66628_half_map_1.map
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Half map: #1

Fileemd_66628_half_map_2.map
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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 / 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: 66 / 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 50451
ExtractionNumber tomograms: 558 / Number images used: 68940 / 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-9x6z:
Structure of the HCoV-229E spike glycoprotein determined by subtomogram averaging

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