7CYD: Alphacoronavirus spike glycoprotein

Cryo-EM structures of Alphacoronavirus spike glycoprotein. Determined by electron microscopy at 3.55 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Human coronavirus 229E
Chains: 3
Atoms: 22,320
Mol. weight: 381.96 kDa
Ligands: NAG
Released: 23 Dec 2020

Explore 7CYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CYD contains 90 α-helices and 150 β-strands across 3 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.

Chains A, B and C: 30 helices, 50 β-strands

Element	Residues	Length	Sheet
α-helix	65-66	2
β-strand	70-81	12	1
β-strand	116-120	5	1
β-strand	130-135	6	2
β-strand	141-144	4	2
β-strand	169-174	6	2
β-strand	177-182	6	2
α-helix	186-187	2
β-strand	192-195	4	1
β-strand	200-201	2	3
β-strand	209-210	2	3
β-strand	216-221	6	2
β-strand	234-245	12	1
β-strand	248-254	7	1
α-helix	258-265	8
α-helix	271-272	2
β-strand	274-278	5	4
β-strand	290-291	2	5
β-strand	304	1	6
β-strand	307-308	2	7
β-strand	323-324	2	7
β-strand	327	1	6
β-strand	346	1	8
β-strand	361-363	3	9
α-helix	372	1
β-strand	380-381	2	8
β-strand	398-400	3	10
β-strand	401-403	3	9
β-strand	409	1	9
β-strand	412-414	3	10
α-helix	415-417	3
β-strand	426-427	2	8
β-strand	447-451	5	5
β-strand	454-463	10	5
β-strand	472-474	3	5
β-strand	480-484	5	5
β-strand	491-496	6	5
β-strand	501-505	5	4
β-strand	510-514	5	4
β-strand	536	1	4
β-strand	546-550	5	11
β-strand	553-556	4	11
β-strand	561-562	2	11
α-helix	566-567	2
β-strand	568	1	12
β-strand	580-585	6	13
β-strand	593-598	6	14
β-strand	604-606	3	15
α-helix	608	1
α-helix	609-613	5
α-helix	617-625	9
α-helix	627-651	25
β-strand	654	1	16
α-helix	656-660	5
α-helix	668-670	3
α-helix	677-680	4
α-helix	691-698	8
α-helix	712-714	3
α-helix	721-723	3
α-helix	724-731	8
β-strand	733-735	3	15
α-helix	736-738	3
α-helix	742-756	15
α-helix	769-780	12
α-helix	789-809	21
α-helix	821-852	32
α-helix	862-868	7
α-helix	871-913	43
α-helix	914-918	5
β-strand	932-941	10	14
β-strand	944-952	9	14
β-strand	957-962	6	13
α-helix	966-968	3
β-strand	981	1	17
β-strand	984	1	18
β-strand	991	1	18
β-strand	994	1	17
α-helix	1001-1003	3
α-helix	1005-1007	3
α-helix	1026-1029	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1116	Human coronavirus 229E	P15423 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>7CYD_1 Spike glycoprotein (chains A, B, C)
MFVLLVAYALLHIAGCQTTNGLNTSYSVCNGCVGYSENVFAVESGGYIPSDFAFNNWFLL
TNTSSVVDGVVRSFQPLLLNCLWSVSGLRFTTGFVYFNGTGRGDCKGFSSDVLSDVIRYN
LNFEENLRRGTILFKTSYGVVVFYCTNNTLVSGDAHIPFGTVLGNFYCFVNTTIGNETTS
AFVGALPKTVREFVISRTGHFYINGYRYFTLGNVEAVNFNVTTAETTDFCTVALASYADV
LVNVSQTSIANIIYCNSVINRLRCDQLSFDVPDGFYSTSPIQSVELPVSIVSLPVYHKHT
FIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAVYANVGRW
SASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIGSLYVSWS
DGDGITGVPQPVEGVSSFMNVTLDKCTKYNIYDVSGVGVIRVSNDTFLNGITYTSTSGNL
LGFKDVTKGTIYSITPCNPPDQLVVYQQAVVGAMLSENFTSYGFSNVVELPKFFYASNGT
YNCTDAVLTYSSFGVCADGSIIAVQPRNVSYDSVSAIVTANLSIPSNWTTSVQVEYLQIT
STPIVVDCSTYVCNGNVRCVELLKQYTSACKTIEDALRNSAMLESADVSEMLTFDKKAFT
LANVSSFGDYNLSSVIPSLPRSGSRVAGRSAIEDILFSKLVTSGLGTVDADYKKCTKGLS
IADLACAQYYNGIMVLPGVADAERMAMYTGSLIGGIALGGLTSAASIPFSLAIQSRLNYV
ALQTDVLQENQKILAASFNKAMTNIVDAFTGVNDAITQTSQALQTVATALNKIQDVVNQQ
GNSLNHLTSQLRQNFQAISSSIQAIYDRLDIIQADQQVDRLITGRLAALNVFVSHTLTKY
TEVRASRQLAQQKVNECVKSQSKRYGFCGNGTHIFSLVNAAPEGLVFLHTVLLPTQYKDV
EAWSGLCVDGRNGYVLRQPNLALYKEGNYYRITSRIMFEPRIPTIADFVQIENCNVTFVN
ISRSELQTIVPEYIDVNKTLQELSYKLPNYTVPDLVVEQYNQTILNLTSEISTLENKSAE
LNYTVQKLQTLIDNINSTLVDLKWLNRVETYIKWPW

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	42

Primary citation

Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Song, X., Shi, Y., Ding, W. et al. Nat Commun (2021) 12:141-141. DOI 10.1038/s41467-020-20401-y · 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
5YL9 1.86 Å, 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core
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…
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…

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