8Y8D: Spike glycoprotein

Structure of HCoV-HKU1C spike in the inactive-1up conformation. Determined by electron microscopy at 3.41 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organism: Human coronavirus HKU1 (isolate N5)
Chains: 3
Atoms: 27,867
Mol. weight: 427.49 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y8D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8D contains 111 α-helices and 268 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: 37 helices, 82 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	34
β-strand	35	1	35
β-strand	49	1	36
β-strand	60-68	9	35
α-helix	69	1
β-strand	75-76	2	35
β-strand	80-81	2	37
β-strand	85-86	2	34
α-helix	87-90	4
β-strand	97	1	38
β-strand	101-107	7	35
β-strand	110-112	3	39
β-strand	117-119	3	39
β-strand	124-127	4	38
β-strand	136-142	7	38
β-strand	145-151	7	38
β-strand	160	1	40
β-strand	161	1	37
β-strand	173	1	40
β-strand	183-190	8	38
β-strand	197-204	8	35
β-strand	208-214	7	35
α-helix	219	1
β-strand	220	1	36
β-strand	221-227	7	35
β-strand	234	1	38
β-strand	240-241	2	37
β-strand	246	1	41
β-strand	250	1	41
β-strand	256-270	15	35
β-strand	276-281	6	35
α-helix	286-294	9
β-strand	302-305	4	42
α-helix	311-313	3
β-strand	316-319	4	43
α-helix	329-333	5
β-strand	337-339	3	44
β-strand	345-349	5	45
β-strand	353-354	2	46
α-helix	356-362	7
β-strand	365-371	7	45
β-strand	383	1	47
β-strand	385-392	8	45
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	45
β-strand	435-437	3	44
β-strand	460-463	4	48
β-strand	467-468	2	49
α-helix	479-481	3
β-strand	494	1	50
α-helix	495-496	2
β-strand	536-537	2	49
β-strand	550-551	2	51
β-strand	564	1	50
α-helix	565-568	4
α-helix	569-571	3
β-strand	572-573	2	51
β-strand	575-578	4	48
β-strand	581-582	2	45
β-strand	585-595	11	45
β-strand	602	1	47
β-strand	603-604	2	46
α-helix	612-614	3
β-strand	620-624	5	43
β-strand	627-631	5	43
β-strand	632-635	4	52
β-strand	647-649	3	52
β-strand	655-659	5	52
β-strand	666-670	5	52
β-strand	678-681	4	42
β-strand	689-691	3	42
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	42
α-helix	719	1
β-strand	720-721	2	42
β-strand	724-725	2	53
β-strand	737	1	53
β-strand	742-746	5	53
β-strand	762-766	5	53
α-helix	772	1
β-strand	773-775	3	28
β-strand	782	1	54
β-strand	785	1	54
β-strand	786-790	5	55
β-strand	794-803	10	56
β-strand	809-812	4	57
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	833-861	29
β-strand	866-868	3	58
α-helix	869-871	3
α-helix	879-881	3
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	57
α-helix	952-964	13
α-helix	979-989	11
α-helix	994-999	6
α-helix	1001-1018	18
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1061-1064	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	56
β-strand	1140-1150	11	56
β-strand	1154-1159	6	55
β-strand	1162-1163	2	59
β-strand	1169-1172	4	59
β-strand	1175-1180	6	55
β-strand	1183-1188	6	55
β-strand	1195	1	55
β-strand	1202-1205	4	59
β-strand	1213-1214	2	59

Chain B: 35 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	60
α-helix	43-45	3
β-strand	49	1	61
β-strand	54-56	3	21
β-strand	60-61	2	62
β-strand	64-68	5	63
α-helix	69	1
β-strand	75-76	2	64
β-strand	80-81	2	65
β-strand	86	1	60
β-strand	97	1	66
β-strand	101-107	7	64
β-strand	109-111	3	67
β-strand	118-120	3	67
β-strand	123-127	5	66
β-strand	136-139	4	66
β-strand	145-151	7	66
β-strand	155	1	68
β-strand	162	1	65
β-strand	175	1	68
β-strand	183-190	8	66
β-strand	197-205	9	64
β-strand	208-214	7	64
β-strand	220	1	61
β-strand	221-227	7	64
β-strand	234-238	5	66
β-strand	240-241	2	65
β-strand	256-260	5	64
β-strand	261-265	5	63
β-strand	266-267	2	69
β-strand	268-269	2	62
β-strand	270	1	70
β-strand	276	1	70
β-strand	280-281	2	69
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	71
β-strand	326	1	72
α-helix	329-333	5
β-strand	337-339	3	73
β-strand	346-350	5	74
β-strand	353	1	72
β-strand	354	1	75
α-helix	356-361	6
β-strand	365-371	7	74
α-helix	376-378	3
β-strand	382-392	11	74
α-helix	398-401	4
α-helix	409-412	4
α-helix	415-417	3
β-strand	422-430	9	74
β-strand	435-437	3	73
α-helix	444-447	4
β-strand	459-463	5	76
β-strand	467-468	2	77
β-strand	477	1	78
α-helix	479-482	4
β-strand	487	1	79
β-strand	492	1	78
β-strand	494	1	80
α-helix	495-496	2
β-strand	504-506	3	81
β-strand	515	1	79
β-strand	516-518	3	81
β-strand	522	1	82
β-strand	527	1	82
β-strand	536-537	2	77
β-strand	548	1	77
β-strand	550-551	2	83
α-helix	553-555	3
β-strand	556	1	84
β-strand	564	1	80
β-strand	567	1	84
α-helix	569-571	3
β-strand	572-573	2	83
β-strand	575-579	5	76
β-strand	581-582	2	74
β-strand	585-597	13	74
β-strand	602-603	2	74
β-strand	604	1	75
β-strand	620	1	85
β-strand	631	1	85
β-strand	634-635	2	86
β-strand	647-648	2	86
β-strand	657-659	3	86
β-strand	666-668	3	86
β-strand	677-681	5	71
β-strand	689-691	3	71
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	71
β-strand	720-721	2	71
β-strand	724-725	2	87
β-strand	737-739	3	87
β-strand	742-746	5	87
β-strand	762-766	5	87
β-strand	773-775	3	58
β-strand	786-791	6	88
β-strand	794-803	10	89
β-strand	809-812	4	90
α-helix	814-818	5
α-helix	823-829	7
α-helix	833-861	29
β-strand	866-868	3	23
α-helix	879-881	3
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	90
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1018	18
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1067-1113	47
β-strand	1131-1137	7	89
β-strand	1140-1150	11	89
β-strand	1153-1159	7	88
β-strand	1162-1163	2	91
β-strand	1169-1172	4	91
β-strand	1175-1179	5	88
β-strand	1184-1188	5	88
β-strand	1195	1	88
α-helix	1199-1201	3
β-strand	1202-1205	4	91
β-strand	1213-1214	2	91

Chain C: 39 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	34-37	4	2
β-strand	49	1	3
α-helix	50-51	2
β-strand	60-68	9	4
α-helix	69	1
β-strand	73-76	4	2
β-strand	80	1	5
β-strand	85-86	2	1
α-helix	87-90	4
β-strand	97	1	6
β-strand	101-107	7	2
β-strand	109-112	4	7
β-strand	117-120	4	7
β-strand	125-127	3	6
β-strand	136-142	7	6
β-strand	145-151	7	6
β-strand	155	1	8
β-strand	161-162	2	5
β-strand	175	1	8
β-strand	183-190	8	6
β-strand	197-205	9	2
β-strand	208-214	7	2
β-strand	220	1	3
β-strand	221-227	7	2
β-strand	234-236	3	6
α-helix	239	1
β-strand	240-241	2	5
β-strand	256-260	5	2
β-strand	261-270	10	4
β-strand	276-278	3	4
β-strand	281	1	4
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	9
α-helix	311-313	3
β-strand	326	1	10
α-helix	329-333	5
β-strand	337-338	2	11
α-helix	341-343	3
β-strand	347-349	3	12
β-strand	353-354	2	10
α-helix	357-361	5
β-strand	365-371	7	12
α-helix	375-377	3
β-strand	383	1	13
β-strand	385-392	8	12
α-helix	398-400	3
α-helix	409-412	4
β-strand	422-430	9	12
β-strand	435-436	2	11
α-helix	443-446	4
β-strand	460	1	14
β-strand	463	1	15
β-strand	468	1	16
α-helix	479-481	3
β-strand	494	1	17
α-helix	495-496	2
α-helix	500-501	2
β-strand	536	1	16
β-strand	551	1	18
β-strand	564	1	17
α-helix	565-568	4
α-helix	569-571	3
β-strand	572	1	18
β-strand	575	1	15
β-strand	578	1	14
β-strand	581-582	2	12
β-strand	585-595	11	12
β-strand	602	1	13
β-strand	603-604	2	10
α-helix	612-614	3
β-strand	620-621	2	19
β-strand	624	1	20
β-strand	627	1	20
β-strand	630-631	2	19
β-strand	632-636	5	21
β-strand	647-649	3	21
β-strand	655-659	5	21
β-strand	666-670	5	21
β-strand	678-681	4	9
α-helix	688	1
β-strand	689-693	5	9
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	9
β-strand	718-721	4	9
β-strand	724-725	2	22
β-strand	736-737	2	22
β-strand	742-746	5	22
β-strand	762-766	5	22
β-strand	773-775	3	23
β-strand	786-789	4	24
α-helix	790-791	2
β-strand	794-796	3	25
β-strand	799-803	5	26
β-strand	809-811	3	27
α-helix	814-817	4
α-helix	823-829	7
α-helix	834-861	28
β-strand	866-868	3	28
β-strand	879	1	29
β-strand	882	1	29
α-helix	905-908	4
α-helix	915-923	9
α-helix	934-940	7
β-strand	944-946	3	27
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-990	12
α-helix	994-999	6
α-helix	1001-1021	21
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1126	1	30
β-strand	1128	1	30
β-strand	1131-1137	7	26
β-strand	1140-1146	7	26
β-strand	1148-1150	3	25
β-strand	1155-1158	4	24
β-strand	1162-1164	3	31
β-strand	1168-1170	3	31
β-strand	1171-1172	2	32
β-strand	1175-1179	5	33
β-strand	1184-1188	5	33
β-strand	1195	1	33
β-strand	1202-1203	2	32
β-strand	1213-1214	2	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1263	Human coronavirus HKU1 (isolate N5)	Q0ZME7

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

>8Y8D_1 Spike glycoprotein (chains A, B, C)
VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGAN
FRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNT
SYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNV
SADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET
LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKP
VATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNL
DKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVN
VTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA
ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINE
EKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTE
ISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCY
SGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS
CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTN
FTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDIT
QLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSPLEDLLFNKVKL
SDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA
AAGVPFPLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATPSALAKIQSVV
NANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQL
SDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSF
KTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT
KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIK
SLN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	26

Primary citation

TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Wang, H., Liu, X., Zhang, X. et al. Cell (2024) 187:4261. DOI 10.1016/j.cell.2024.06.016 · PubMed

Other PDB entries of the same protein (UniProt Q0ZME7), best resolution first:

9YXW 2.6 Å, Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab
8Y8C 2.95 Å, Structure of HCoV-HKU1C spike in the inactive-closed conformation
8Y8B 3.01 Å, Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan
8Y88 3.03 Å, Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
8Y8F 3.07 Å, Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
8Y8A 3.19 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
9YGP 3.2 Å, HCoV-HKU1 C S 2P in complex with H501-018 Fab (local cryoEM)
8Y8G 3.23 Å, Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
8Y87 3.26 Å, Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
8Y89 3.32 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
9YGN 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 1, global cryoEM)
9YGO 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 2, global cryoEM)

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