7CYC: Alphacoronavirus spike glycoprotein

Cryo-EM structures of Alphacoronavirus spike glycoprotein. Determined by electron microscopy at 3.21 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 3.21 Å
Organism: Human coronavirus 229E
Chains: 3
Atoms: 22,521
Mol. weight: 386.32 kDa
Ligands: NAG
Released: 23 Dec 2020

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

Secondary structure: helices and β-sheets

7CYC contains 85 α-helices and 184 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.

Chain A: 29 helices, 62 β-strands

Element	Residues	Length	Sheet
α-helix	64	1
β-strand	65	1	1
α-helix	66	1
β-strand	70-76	7	2
β-strand	94-95	2	3
β-strand	116-120	5	4
β-strand	130-135	6	3
β-strand	139-146	8	3
β-strand	167-174	8	3
β-strand	177-178	2	3
β-strand	181-182	2	3
β-strand	192-196	5	4
β-strand	200-203	4	4
β-strand	206-210	5	4
β-strand	216-221	6	3
β-strand	231-235	5	4
β-strand	237-245	9	2
β-strand	248-254	7	2
α-helix	258-265	8
α-helix	271-272	2
β-strand	274-278	5	5
β-strand	288-291	4	6
β-strand	301-302	2	7
β-strand	305	1	8
β-strand	328	1	8
β-strand	339	1	9
β-strand	345-346	2	10
β-strand	347-348	2	7
α-helix	354-356	3
β-strand	360-364	5	11
β-strand	380-384	5	10
β-strand	387	1	9
β-strand	388	1	12
β-strand	396-404	9	11
β-strand	409-417	9	11
β-strand	420-427	8	10
β-strand	447-451	5	6
β-strand	454-458	5	6
β-strand	459-463	5	13
β-strand	472-474	3	13
β-strand	480-484	5	13
β-strand	491-495	5	13
β-strand	501-506	6	5
β-strand	509-515	7	5
β-strand	526-530	5	5
β-strand	533-537	5	5
β-strand	548-549	2	14
β-strand	553-555	3	14
β-strand	561-563	3	14
β-strand	567-568	2	15
β-strand	581-585	5	16
β-strand	588-598	11	17
β-strand	604-606	3	18
α-helix	608-613	6
α-helix	617-624	8
α-helix	627-651	25
β-strand	653-654	2	19
α-helix	656-659	4
α-helix	660-662	3
α-helix	664-666	3
α-helix	677	1
β-strand	678	1	20
α-helix	679-680	2
β-strand	688	1	20
α-helix	691-699	9
α-helix	712-714	3
α-helix	721-723	3
α-helix	724-731	8
β-strand	733-735	3	18
α-helix	736-738	3
α-helix	742-754	13
α-helix	769-780	12
α-helix	789-809	21
α-helix	821-847	27
α-helix	850-852	3
α-helix	862-868	7
α-helix	871-913	43
α-helix	914-918	5
β-strand	933-941	9	17
β-strand	944-954	11	17
β-strand	957-961	5	16
β-strand	966-967	2	21
β-strand	973-976	4	21
β-strand	981-984	4	22
β-strand	991-994	4	22
β-strand	1000-1001	2	22
α-helix	1005-1007	3
β-strand	1008-1011	4	21
α-helix	1014-1015	2
β-strand	1019-1020	2	21
α-helix	1023-1029	7

Chains B and C: 28 helices, 61 β-strands

Element	Residues	Length	Sheet
α-helix	64-66	3
β-strand	70-76	7	23
β-strand	94-95	2	24
β-strand	116-120	5	25
β-strand	130-135	6	24
β-strand	139-146	8	24
β-strand	167-174	8	24
β-strand	177-178	2	24
β-strand	181-182	2	24
β-strand	192-196	5	25
β-strand	200-203	4	25
β-strand	206-210	5	25
β-strand	216-221	6	24
β-strand	231-235	5	25
β-strand	237-245	9	23
β-strand	248-254	7	23
α-helix	258-265	8
α-helix	271-272	2
β-strand	274-278	5	26
β-strand	288-291	4	27
β-strand	301-302	2	28
β-strand	305	1	29
β-strand	328	1	29
β-strand	339	1	30
β-strand	345-346	2	31
β-strand	347-348	2	28
α-helix	354-356	3
β-strand	360-364	5	32
β-strand	380-384	5	31
β-strand	387	1	30
β-strand	388	1	33
β-strand	396-404	9	32
β-strand	409-417	9	32
β-strand	420-427	8	31
β-strand	447-451	5	27
β-strand	454-458	5	27
β-strand	459-463	5	1
β-strand	472-474	3	1
β-strand	480-484	5	1
β-strand	491-495	5	1
β-strand	501-506	6	26
β-strand	509-515	7	26
β-strand	526-530	5	26
β-strand	533-537	5	26
β-strand	548-549	2	34
β-strand	553-555	3	34
β-strand	561-563	3	34
β-strand	567-568	2	19
β-strand	581-585	5	35
β-strand	588-598	11	36
β-strand	604-606	3	37
α-helix	608-613	6
α-helix	617-624	8
α-helix	627-651	25
β-strand	653-654	2	38
α-helix	656-659	4
α-helix	660-662	3
α-helix	664-666	3
α-helix	677	1
β-strand	678	1	39
α-helix	679-680	2
β-strand	688	1	39
α-helix	691-699	9
α-helix	712-714	3
α-helix	721-723	3
α-helix	724-731	8
β-strand	733-735	3	37
α-helix	736-738	3
α-helix	742-754	13
α-helix	769-780	12
α-helix	789-809	21
α-helix	821-847	27
α-helix	850-852	3
α-helix	862-868	7
α-helix	871-913	43
α-helix	914-918	5
β-strand	933-941	9	36
β-strand	944-954	11	36
β-strand	957-961	5	35
β-strand	966-967	2	40
β-strand	973-976	4	40
β-strand	981-984	4	41
β-strand	991-994	4	41
β-strand	1000-1001	2	41
α-helix	1005-1007	3
β-strand	1008-1011	4	40
α-helix	1014-1015	2
β-strand	1019-1020	2	40
α-helix	1023-1029	7

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

>7CYC_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	48

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
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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