5YL9: Spike glycoprotein

1.86 Angstrom crystal structure of human Coronavirus 229E fusion core. Determined by X-ray diffraction at 1.86 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Human coronavirus 229E
Chains: 2
Atoms: 1,232
Mol. weight: 16.25 kDa
Released: 26 Sept 2018

Explore 5YL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YL9 contains 4 α-helices and 0 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	786-871	86

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1058-1060	3
α-helix	1062-1064	3
α-helix	1068-1096	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A	protein	89	Human coronavirus 229E	P15423 (AlphaFold model)
Spike glycoprotein	B	protein	59	Human coronavirus 229E	P15423 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YL9_1 Spike glycoprotein (chains A)
SDVLQENQKILAASFNKAMTNIVDAFTGVNDAITQTSQALQTVATALNKIQDVVNQQGNS
LNHLTSQLRQNFQAISSSIQAIYDRLDTI

Sequence of entity 2 (B), FASTA

>5YL9_2 Spike glycoprotein (chains B)
SGGRGGVPDLVVEQYNQTILNLTSEISTLENKSAELNYTVQKLQTLIDNINSTLVDLKW

Primary citation

Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 angstrom resolution. Yan, L., Meng, B., Xiang, J. et al. Acta Crystallogr D Struct Biol (2018) 74:841-851. DOI 10.1107/S2059798318008318 · PubMed

Other PDB entries of the same protein (UniProt P15423 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
5ZUV 2.21 Å, Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs…
7YI6 2.28 Å, bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
5ZHY 2.44 Å, Structural characterization of the HCoV-229E fusion core
6U7H 3.1 Å, Cryo-EM structure of the HCoV-229E spike glycoprotein
7CYC 3.21 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
6ATK 3.5 Å, Crystal structure of the human coronavirus 229E spike protein receptor binding domain in…
7CYD 3.55 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
8WDE 3.6 Å, CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN…
7VNG 3.8 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…
7VN9 4.49 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…

Browse structure collections

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