8WDE: Spike protein of human CoV 229E

CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN (composite map). Determined by electron microscopy at 3.6 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Human coronavirus 229E, Homo sapiens
Chains: 5
Atoms: 33,348
Mol. weight: 607.44 kDa
Ligands: NAG
Released: 5 Mar 2025

Explore 8WDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WDE contains 173 α-helices and 208 β-strands across 5 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, 49 β-strands

Element	Residues	Length	Sheet
α-helix	42	1
β-strand	43	1	1
β-strand	47	1	1
α-helix	48-49	2
β-strand	61	1	2
β-strand	65-66	2	3
β-strand	69-85	17	2
β-strand	95-96	2	4
β-strand	116-121	6	2
α-helix	126-128	3
β-strand	131-135	5	4
β-strand	140-145	6	4
β-strand	167-172	6	4
β-strand	179-185	7	4
α-helix	186-187	2
β-strand	192-196	5	2
β-strand	200-203	4	2
β-strand	206-210	5	2
β-strand	216-220	5	4
α-helix	226-228	3
β-strand	230-245	16	2
β-strand	248-254	7	2
α-helix	258-266	9
β-strand	274-278	5	5
α-helix	280-283	4
β-strand	288-291	4	6
β-strand	297	1	7
β-strand	299-309	11	8
β-strand	317	1	9
β-strand	323-329	7	8
α-helix	334-336	3
β-strand	339-340	2	8
β-strand	345-352	8	8
β-strand	360-364	5	8
α-helix	375-377	3
β-strand	381-388	8	8
β-strand	396-404	9	8
β-strand	408-427	20	8
β-strand	434	1	7
β-strand	446-451	6	6
β-strand	454-462	9	6
β-strand	472-474	3	6
β-strand	480-485	6	6
β-strand	490-495	6	6
β-strand	501-506	6	5
β-strand	509-515	7	5
β-strand	526-529	4	5
β-strand	534-537	4	5
β-strand	546-550	5	10
β-strand	553-556	4	10
β-strand	561-563	3	10
β-strand	584-598	15	11
β-strand	604-605	2	12
α-helix	608-613	6
α-helix	617-623	7
α-helix	631-651	21
α-helix	656-659	4
α-helix	660-662	3
α-helix	664-667	4
α-helix	672-674	3
α-helix	677-679	3
α-helix	691-699	9
α-helix	701-703	3
α-helix	715-717	3
α-helix	721-723	3
α-helix	724-729	6
β-strand	734-735	2	12
α-helix	736-738	3
α-helix	742-756	15
α-helix	769-779	11
α-helix	788-810	23
α-helix	820-850	31
α-helix	862-868	7
α-helix	871-917	47
β-strand	926	1	13
β-strand	929	1	13
β-strand	932-940	9	11
β-strand	944-958	15	11

Chain B: 29 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	44-46	3
α-helix	47-49	3
β-strand	61	1	14
β-strand	65-66	2	6
β-strand	69-86	18	14
β-strand	95-96	2	15
β-strand	116-121	6	14
α-helix	127-129	3
β-strand	131-136	6	15
β-strand	139-146	8	15
β-strand	167-172	6	15
β-strand	179-185	7	15
α-helix	186-187	2
β-strand	192-196	5	14
β-strand	200-203	4	14
β-strand	206-210	5	14
β-strand	216-220	5	15
β-strand	229-245	17	14
β-strand	248-254	7	14
α-helix	258-266	9
β-strand	274-278	5	16
α-helix	280-283	4
β-strand	288-291	4	17
β-strand	300-305	6	18
β-strand	328-329	2	18
β-strand	345-350	6	18
α-helix	375-377	3
β-strand	381-388	8	18
β-strand	397-398	2	18
β-strand	401-404	4	19
β-strand	408-411	4	19
β-strand	415-427	13	18
β-strand	447-451	5	17
β-strand	454-458	5	17
β-strand	459-463	5	20
β-strand	472-474	3	20
β-strand	480-484	5	20
β-strand	491-495	5	20
β-strand	501-506	6	16
β-strand	509-514	6	16
β-strand	526-529	4	16
β-strand	534-537	4	16
β-strand	548-550	3	21
β-strand	553-555	3	21
α-helix	556	1
β-strand	561-563	3	21
β-strand	584-598	15	22
β-strand	606	1	23
α-helix	608-613	6
α-helix	617-623	7
α-helix	631-651	21
α-helix	656-660	5
α-helix	664-667	4
α-helix	677	1
β-strand	678	1	24
α-helix	679	1
β-strand	688	1	24
α-helix	691-699	9
α-helix	701-702	2
α-helix	721-722	2
α-helix	724-729	6
β-strand	733	1	23
α-helix	735-738	4
α-helix	742-754	13
α-helix	770-777	8
α-helix	788-810	23
α-helix	820-849	30
α-helix	850-852	3
α-helix	862-868	7
α-helix	871-913	43
α-helix	914-918	5
β-strand	926	1	25
β-strand	929	1	25
β-strand	932-941	10	22
β-strand	944-958	15	22

Chain C: 28 helices, 48 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
β-strand	43	1	26
β-strand	47	1	26
α-helix	48-49	2
β-strand	61	1	27
β-strand	65-66	2	20
β-strand	69-86	18	27
α-helix	87-89	3
β-strand	95-96	2	28
β-strand	116-120	5	27
α-helix	126-128	3
β-strand	131-136	6	28
β-strand	139-146	8	28
β-strand	167-173	7	28
β-strand	179-185	7	28
β-strand	192-196	5	27
β-strand	200-203	4	27
β-strand	206-210	5	27
β-strand	214-220	7	28
β-strand	229-245	17	27
β-strand	248-254	7	27
α-helix	258-266	9
β-strand	274	1	29
β-strand	277-278	2	29
α-helix	280-283	4
β-strand	288-289	2	30
β-strand	299-306	8	31
β-strand	327-329	3	31
β-strand	345-350	6	31
α-helix	375-377	3
β-strand	381-388	8	32
β-strand	397-404	8	32
β-strand	408-426	19	32
β-strand	427	1	31
β-strand	443	1	3
β-strand	447-449	3	30
α-helix	451-453	3
β-strand	456-458	3	30
β-strand	459-463	5	3
β-strand	472-474	3	3
β-strand	480-485	6	3
β-strand	490-495	6	3
α-helix	496	1
β-strand	501-506	6	29
β-strand	509-515	7	29
β-strand	526-530	5	29
β-strand	533-537	5	29
β-strand	548-549	2	33
β-strand	554-555	2	33
β-strand	561-562	2	33
β-strand	584-598	15	34
β-strand	604-606	3	35
α-helix	608-612	5
α-helix	617-623	7
α-helix	629-651	23
α-helix	656-660	5
α-helix	664-667	4
α-helix	677-679	3
α-helix	691-699	9
α-helix	701-703	3
α-helix	721-723	3
α-helix	724-730	7
β-strand	733-735	3	35
α-helix	736-738	3
α-helix	742-757	16
α-helix	769-780	12
α-helix	782-785	4
α-helix	788-810	23
α-helix	823-849	27
α-helix	850-852	3
α-helix	862-868	7
α-helix	871-917	47
β-strand	926-927	2	36
β-strand	929	1	36
β-strand	932-941	10	34
β-strand	944-958	15	34

Chain D: 47 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
β-strand	80-91	12	37
β-strand	102-113	12	37
β-strand	117-123	7	38
β-strand	128-129	2	37
β-strand	132	1	39
β-strand	135	1	39
β-strand	138	1	37
α-helix	148-149	2
β-strand	150-156	7	38
β-strand	161-170	10	38
α-helix	171	1
β-strand	175-185	11	37
β-strand	192	1	40
β-strand	195-200	6	41
β-strand	203-208	6	41
β-strand	211	1	40
α-helix	217-219	3
β-strand	223	1	38
β-strand	231	1	42
β-strand	233-240	8	37
β-strand	244-247	4	41
β-strand	251	1	43
β-strand	256-258	3	37
β-strand	261-268	8	37
β-strand	269	1	43
α-helix	270-272	3
β-strand	275	1	42
α-helix	277-279	3
β-strand	282-285	4	41
β-strand	288-293	6	9
β-strand	299-304	6	9
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	9
β-strand	353-354	2	9
β-strand	359-363	5	9
α-helix	364-366	3
α-helix	376-391	16
β-strand	395	1	44
β-strand	399	1	44
β-strand	400-401	2	45
α-helix	404-406	3
α-helix	407-425	19
α-helix	427-429	3
α-helix	431-433	3
α-helix	434-435	2
α-helix	436-440	5
α-helix	441-447	7
α-helix	459-461	3
α-helix	465-469	5
α-helix	474	1
α-helix	475-479	5
α-helix	480-490	11
α-helix	493-507	15
β-strand	511-512	2	45
α-helix	514-528	15
α-helix	536-544	9
β-strand	550-555	6	46
β-strand	560-565	6	46
β-strand	586-592	7	47
β-strand	595-602	8	47
β-strand	606-608	3	46
α-helix	610-612	3
β-strand	620-622	3	47
α-helix	624-626	3
β-strand	631-634	4	46
α-helix	636-648	13
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-682	7
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-763	17
α-helix	766-780	15
α-helix	793-802	10
α-helix	807-818	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-847	10
α-helix	859-868	10
α-helix	870-872	3
α-helix	873-889	17
α-helix	898-906	9
α-helix	912-923	12
α-helix	933-964	32

Chain E: 40 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	82-92	11	48
β-strand	102-111	10	48
β-strand	192-195	4	49
β-strand	208-211	4	49
α-helix	217-219	3
β-strand	230-231	2	50
β-strand	232-237	6	48
α-helix	271-273	3
β-strand	275-276	2	50
α-helix	277-279	3
β-strand	283	1	49
α-helix	321-331	11
β-strand	342-346	5	51
β-strand	353-354	2	51
β-strand	359-363	5	51
α-helix	364-366	3
α-helix	376-391	16
β-strand	395	1	52
β-strand	399	1	52
β-strand	400-401	2	53
α-helix	404-406	3
α-helix	407-425	19
α-helix	427-429	3
α-helix	431-433	3
α-helix	434-435	2
α-helix	436-440	5
α-helix	441-447	7
α-helix	465-469	5
α-helix	474-490	17
α-helix	493-507	15
β-strand	511-512	2	53
α-helix	515-528	14
α-helix	536-544	9
β-strand	550-555	6	54
β-strand	560-565	6	54
β-strand	586-588	3	55
β-strand	590-592	3	56
β-strand	595-596	2	56
α-helix	597-599	3
β-strand	600-602	3	55
β-strand	606-608	3	54
α-helix	610-612	3
β-strand	620-622	3	56
α-helix	624-626	3
β-strand	631-634	4	54
α-helix	636-648	13
α-helix	655-670	16
α-helix	676-682	7
α-helix	683-688	6
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	793-801	9
α-helix	807-818	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-849	12
α-helix	859-868	10
α-helix	870-889	20
α-helix	898-906	9
α-helix	912-925	14
α-helix	926-928	3
α-helix	933-965	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1165	Human coronavirus 229E	P15423 (AlphaFold model)
Aminopeptidase N	D, E	protein	943	Homo sapiens	P15144 (AlphaFold model)

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

>8WDE_1 Spike glycoprotein (chains A, B, C)
GTQTTNGLNTSYSVCNGCVGYSENVFAVESGGYIPSDFAFNNWFLLTNTSSVVDGVVRSF
QPLLLNCLWSVSGLRFTTGFVYFNGTGRGDCKGFSSDVLSDVIRYNLNFEENLRRGTILF
KTSYGVVVFYCTNNTLVSGDAHIPFGTVLGNFYCFVNTTIGTETTSAFVGALPKTVREFV
ISRTGHFYINGYRYFTLGNVEAVNFNVTTAETTDFFTVALASYADVLVNVSQTSIANIIY
CNSVINRLRCDQLSFYVPDGFYSTSPIQSVELPVSIVSLPVYHKHMFIVLYVDFKPQSGG
GKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAVYANVGRWSASINTGNCPFSFG
KVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIGTLYVSWSDGDGITGVPQPVEG
VSSFMNVTLDKCTKYNIYDVSGVGVIRVSNDTFLNGITYTSTSGNLLGFKDVTKGTIYSI
TPCNPPDQLVVYQQAVVGAMLSENFTSYGFSNVVELPKFFYASNGTYNCTDAVLTYSSFG
VCADGSIIAVQPRNVSYDSVSAIVTANLSIPSNWTISVQVEYLQITSTPIVVDCSTYVCN
GNVRCVELLKQYTSACKTIEDALRNSARLESADVSEMLTFDKKAFTLANVSSFGDYNLSS
VIPSLPTSGSRVAGRSAIEDILFSKIVTSGLGTVDADYKNCTKGLSIADLACAQYYNGIM
VLPGVADAERMAMYTGSLIGGIALGGLTSAVSIPFSLAIQARLNYVALQTDVLQENQKIL
AASFNKAMTNIVDAFTGVNDAITQTSQALQTVATALNKIQDVVNQQGNSLNHLTSQLRQN
FQAISSSIQAIYDRLDPPQADQQVDRLITGRLAALNVFVSHTLTKYTEVRASRQLAQQKV
NECVKSQSKRYGFCGNGTHIFSIVNAAPEGLVFLHTVLLPTQYKDVEAWSGLCVDGTNGY
VLRQPNLALYKEGNYYRITSRIMFEPRIPTMADFVQIENCNVTFVNISRSELQTIVPEYI
DVNKTLQELSYKLPNYTVPDLVVEQYNQTILNLTSEISTLENKSAELNYTVQKLQTLIDN
INSTLVDLKWLNRVETYIKGSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTF
LGHHHHHHHHGLNDIFEAQKIEWHE

Sequence of entity 2 (D, E), FASTA

>8WDE_2 Aminopeptidase N (chains D, E)
DQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSK
KLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGE
LADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTA
LSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWAR
PSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYREN
SLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYA
EPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLR
MLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTL
QMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDV
RAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDA
FNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQ
VTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNN
NPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYL
SYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAV
TRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTEN
SKQDNSADIQHSGRPLESRGPFEQKLISEEDLNMHTGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	20

Primary citation

Molecular basis of host recognition of human coronavirus 229E. Tsai, Y.X., Chien, Y.C., Hsu, M.F. et al. Nat Commun (2025) 16:2045-2045. DOI 10.1038/s41467-025-57359-8 · 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…
7CYD 3.55 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
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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