8Y8C: Spike glycoprotein

Structure of HCoV-HKU1C spike in the inactive-closed conformation. Determined by electron microscopy at 2.95 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 2.95 Å
Organism: Human coronavirus HKU1 (isolate N5)
Chains: 3
Atoms: 27,789
Mol. weight: 426.26 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8C contains 124 α-helices and 280 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: 41 helices, 94 β-strands

Element	Residues	Length	Sheet
β-strand	39	1	1
β-strand	49	1	2
α-helix	50-51	2
β-strand	55	1	3
β-strand	60-68	9	4
α-helix	69	1
β-strand	73	1	1
β-strand	75-76	2	5
β-strand	80-81	2	6
α-helix	87-90	4
β-strand	96-97	2	7
β-strand	101-107	7	5
β-strand	109	1	8
β-strand	120	1	8
β-strand	123-127	5	7
β-strand	136-142	7	7
β-strand	145-151	7	7
β-strand	155	1	9
β-strand	161-162	2	6
β-strand	175	1	9
β-strand	185-190	6	7
β-strand	197-205	9	5
β-strand	208-214	7	5
β-strand	220	1	2
β-strand	221-227	7	5
β-strand	234-238	5	7
α-helix	239	1
β-strand	240-241	2	6
β-strand	256-260	5	5
β-strand	261-270	10	4
β-strand	276-281	6	4
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	10
β-strand	309-310	2	11
α-helix	311-313	3
β-strand	316-319	4	12
β-strand	326	1	13
α-helix	329-333	5
β-strand	337-339	3	14
α-helix	341-343	3
β-strand	345-349	5	15
β-strand	353	1	13
β-strand	354	1	16
α-helix	356-361	6
β-strand	365-371	7	15
α-helix	375-377	3
β-strand	385-392	8	15
α-helix	398-401	4
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	15
β-strand	435-437	3	14
α-helix	446-448	3
β-strand	459-463	5	17
β-strand	466-468	3	18
β-strand	477	1	19
α-helix	479-482	4
β-strand	487	1	20
α-helix	489-491	3
β-strand	492	1	19
α-helix	494-496	3
α-helix	501-503	3
β-strand	504-505	2	21
β-strand	515	1	20
β-strand	517-518	2	21
β-strand	536-538	3	18
β-strand	550-551	2	22
β-strand	556-557	2	23
β-strand	566-567	2	23
β-strand	572-573	2	22
β-strand	575-579	5	17
β-strand	581-582	2	15
β-strand	585-595	11	15
β-strand	604	1	16
α-helix	614-615	2
β-strand	616	1	24
β-strand	620-624	5	12
β-strand	627-631	5	12
β-strand	632	1	25
β-strand	633	1	24
β-strand	636	1	26
β-strand	647-649	3	26
β-strand	655-659	5	26
β-strand	666-667	2	26
β-strand	670	1	25
α-helix	671-673	3
β-strand	674-675	2	11
β-strand	678-681	4	10
β-strand	689-693	5	10
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	10
β-strand	718-721	4	10
β-strand	724-731	8	27
β-strand	737-739	3	27
β-strand	742-746	5	27
β-strand	762-767	6	27
β-strand	773-775	3	28
β-strand	782	1	29
β-strand	785	1	29
β-strand	786-804	19	30
β-strand	809-812	4	31
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	835-861	27
β-strand	866-868	3	32
β-strand	878-879	2	33
β-strand	882-883	2	33
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	31
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1002-1016	15
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	30
β-strand	1140-1158	19	30
β-strand	1159	1	34
β-strand	1162-1164	3	35
β-strand	1168-1172	5	35
β-strand	1175-1179	5	34
β-strand	1184-1188	5	34
β-strand	1195	1	34
β-strand	1202-1205	4	35
β-strand	1213-1214	2	35

Chain B: 43 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	36
β-strand	25	1	37
α-helix	33	1
β-strand	34-35	2	38
α-helix	36	1
β-strand	49	1	39
α-helix	50-51	2
β-strand	55	1	40
β-strand	60-61	2	41
β-strand	64-68	5	42
α-helix	69	1
β-strand	75-76	2	38
β-strand	80-81	2	43
β-strand	85	1	37
α-helix	88-90	3
β-strand	96-97	2	44
β-strand	101-107	7	38
β-strand	109-113	5	45
β-strand	116-120	5	45
β-strand	123-127	5	44
β-strand	136-141	6	44
β-strand	145-151	7	44
β-strand	155	1	46
β-strand	156	1	36
β-strand	161-162	2	43
β-strand	175	1	46
α-helix	180-182	3
β-strand	183-190	8	44
β-strand	197-205	9	38
β-strand	208-214	7	38
β-strand	220	1	39
β-strand	221-227	7	38
β-strand	234-238	5	44
β-strand	240-241	2	43
β-strand	256-260	5	38
β-strand	261-265	5	42
β-strand	266	1	47
β-strand	268-270	3	41
β-strand	276-278	3	41
β-strand	281	1	47
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	48
β-strand	309-310	2	49
α-helix	311-313	3
β-strand	316-319	4	3
β-strand	326	1	50
α-helix	329-333	5
β-strand	337-339	3	51
α-helix	341-343	3
β-strand	345-349	5	52
β-strand	353	1	50
β-strand	354	1	53
α-helix	357-362	6
β-strand	365-371	7	52
α-helix	375-377	3
β-strand	382-383	2	54
β-strand	385-392	8	52
α-helix	398-400	3
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	52
β-strand	435-437	3	51
α-helix	443-446	4
β-strand	459-463	5	55
β-strand	467-468	2	56
β-strand	477	1	57
β-strand	492	1	57
β-strand	494	1	58
α-helix	495-496	2
β-strand	536-537	2	56
β-strand	550-551	2	59
α-helix	553-555	3
β-strand	556	1	60
β-strand	564	1	58
β-strand	567	1	60
α-helix	569-571	3
β-strand	572-573	2	59
β-strand	575-579	5	55
β-strand	581-582	2	52
β-strand	585-595	11	52
β-strand	602-603	2	54
β-strand	604	1	53
β-strand	619-624	6	3
β-strand	627-636	10	3
β-strand	647-649	3	3
β-strand	655-659	5	3
β-strand	666-670	5	3
α-helix	671-673	3
β-strand	674-675	2	49
β-strand	678-681	4	48
β-strand	689-693	5	48
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	48
β-strand	718-721	4	48
β-strand	724-731	8	61
β-strand	737-739	3	61
β-strand	742-746	5	61
β-strand	762-767	6	61
β-strand	773-775	3	32
β-strand	782	1	62
β-strand	785	1	62
β-strand	786-791	6	63
β-strand	794-804	11	64
β-strand	809-812	4	65
α-helix	815-818	4
α-helix	823-829	7
α-helix	836-861	26
β-strand	866-868	3	66
α-helix	869-871	3
β-strand	879	1	67
β-strand	882	1	67
α-helix	885-887	3
α-helix	902-909	8
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	65
α-helix	947-948	2
α-helix	952-964	13
α-helix	972-974	3
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1018	18
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	64
β-strand	1140-1150	11	64
β-strand	1153-1158	6	63
β-strand	1159	1	68
β-strand	1162-1163	2	69
β-strand	1169	1	70
β-strand	1170	1	69
β-strand	1172	1	71
β-strand	1175-1180	6	68
β-strand	1183-1188	6	68
β-strand	1195	1	68
α-helix	1199-1201	3
β-strand	1202	1	71
β-strand	1205	1	70
β-strand	1213-1214	2	69

Chain C: 40 helices, 85 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	72
α-helix	32-36	5
β-strand	49	1	73
β-strand	54-55	2	26
β-strand	59-68	10	74
α-helix	69	1
β-strand	76	1	75
β-strand	80-81	2	76
α-helix	87-90	4
β-strand	96-97	2	77
β-strand	101-107	7	75
β-strand	109-113	5	78
β-strand	116-120	5	78
β-strand	123-127	5	77
β-strand	136-141	6	77
β-strand	145-151	7	77
β-strand	155	1	79
β-strand	156	1	72
β-strand	161-162	2	76
β-strand	175	1	79
α-helix	180-182	3
β-strand	183-190	8	77
β-strand	197-205	9	75
β-strand	208-214	7	75
β-strand	220	1	73
β-strand	221-227	7	75
β-strand	234-238	5	77
β-strand	240-241	2	76
β-strand	256-260	5	75
β-strand	261-270	10	74
β-strand	276-278	3	74
β-strand	281	1	74
α-helix	286-294	9
β-strand	302-305	4	80
β-strand	309-310	2	81
α-helix	311-313	3
β-strand	316-319	4	82
α-helix	329-333	5
β-strand	337-338	2	83
β-strand	340	1	84
β-strand	343	1	84
β-strand	345-349	5	85
β-strand	353-354	2	86
α-helix	357-362	6
β-strand	365-371	7	85
α-helix	375-377	3
β-strand	382-383	2	86
β-strand	385-392	8	85
α-helix	398-400	3
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	85
β-strand	435-436	2	83
α-helix	443-447	5
β-strand	459-463	5	87
β-strand	466-468	3	88
α-helix	479-482	4
α-helix	494-496	3
α-helix	530-532	3
β-strand	536-538	3	88
β-strand	550-551	2	89
α-helix	553-555	3
β-strand	556-557	2	90
β-strand	566-567	2	90
α-helix	569-571	3
β-strand	572-573	2	89
β-strand	575-579	5	87
β-strand	585-595	11	85
β-strand	602-604	3	86
β-strand	620-624	5	82
β-strand	627-631	5	82
β-strand	632-636	5	40
β-strand	647-649	3	40
β-strand	655-659	5	40
β-strand	666-670	5	40
α-helix	671-673	3
β-strand	674-675	2	81
β-strand	678-681	4	80
α-helix	688	1
β-strand	689-693	5	80
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	80
β-strand	718-721	4	80
β-strand	724-731	8	91
β-strand	736-739	4	91
β-strand	742-746	5	91
β-strand	762-767	6	91
β-strand	773-775	3	66
β-strand	782	1	92
β-strand	785	1	92
β-strand	786-804	19	93
β-strand	809-812	4	94
α-helix	814-819	6
α-helix	823-829	7
α-helix	834-861	28
β-strand	866-868	3	28
β-strand	878-879	2	95
β-strand	882-883	2	95
α-helix	885-887	3
α-helix	902-909	8
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	94
α-helix	947-948	2
α-helix	952-964	13
α-helix	972-974	3
α-helix	979-988	10
α-helix	994-998	5
α-helix	1001-1018	18
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	93
β-strand	1140-1158	19	93
β-strand	1159	1	96
β-strand	1162-1164	3	97
β-strand	1168-1172	5	97
β-strand	1175-1179	5	96
β-strand	1184-1188	5	96
β-strand	1195	1	96
β-strand	1202-1205	4	97
β-strand	1213-1214	2	97

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

>8Y8C_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	25

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
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)
8Y8D 3.41 Å, Structure of HCoV-HKU1C spike in the inactive-1up conformation

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