8Y87: Spike glycoprotein

Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2. Determined by electron microscopy at 3.26 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Human coronavirus HKU1 (isolate N5), Homo sapiens
Chains: 4
Atoms: 29,531
Mol. weight: 469.31 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y87 contains 122 α-helices and 290 β-strands across 4 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: 38 helices, 87 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
β-strand	35	1	3
β-strand	49	1	4
β-strand	60-67	8	5
α-helix	68-69	2
β-strand	75-76	2	3
β-strand	80-81	2	6
β-strand	85-86	2	2
α-helix	88-90	3
β-strand	97	1	7
β-strand	101-107	7	3
β-strand	110-112	3	8
β-strand	117-119	3	8
β-strand	125-127	3	7
β-strand	136-138	3	7
β-strand	141	1	7
β-strand	145-151	7	7
β-strand	155	1	9
β-strand	156	1	1
β-strand	162	1	6
β-strand	175	1	9
β-strand	183-190	8	7
β-strand	197-205	9	3
β-strand	208-214	7	3
β-strand	220	1	4
β-strand	221-227	7	3
β-strand	234	1	7
β-strand	240-241	2	6
β-strand	246	1	10
β-strand	250	1	10
β-strand	256-260	5	3
β-strand	262-270	9	5
β-strand	276-281	6	5
α-helix	286-294	9
β-strand	302-305	4	11
α-helix	311-313	3
β-strand	316-319	4	12
β-strand	326	1	13
α-helix	329-333	5
β-strand	337-338	2	14
α-helix	339-340	2
α-helix	341-343	3
β-strand	345-349	5	15
β-strand	353-354	2	13
α-helix	356-362	7
β-strand	365-371	7	15
β-strand	383-392	10	15
α-helix	398-400	3
α-helix	409-412	4
β-strand	422-430	9	15
β-strand	435-436	2	14
β-strand	460-463	4	16
β-strand	466-468	3	17
α-helix	479-481	3
β-strand	494	1	18
α-helix	495-496	2
β-strand	536-538	3	17
β-strand	550-551	2	19
β-strand	564	1	18
α-helix	565-568	4
β-strand	572-573	2	19
β-strand	575-578	4	16
β-strand	581-582	2	15
β-strand	585-597	13	15
β-strand	602	1	15
β-strand	603-604	2	13
α-helix	612-615	4
β-strand	620-624	5	12
β-strand	627-631	5	12
β-strand	632-635	4	20
β-strand	647-649	3	20
β-strand	655-659	5	20
β-strand	666-670	5	20
β-strand	678-681	4	11
α-helix	688	1
β-strand	689-691	3	11
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	11
α-helix	719	1
β-strand	720-721	2	11
β-strand	724-725	2	21
β-strand	737	1	21
β-strand	742-746	5	21
β-strand	762-766	5	21
β-strand	773-775	3	22
β-strand	782	1	23
β-strand	785	1	23
β-strand	786-791	6	24
β-strand	794-803	10	25
β-strand	809-812	4	26
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	27
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	934-941	8
β-strand	943-946	4	26
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	1059-1062	4
α-helix	1067-1069	3
α-helix	1071-1113	43
β-strand	1131-1137	7	25
β-strand	1140-1150	11	25
β-strand	1153-1158	6	24
β-strand	1159	1	28
β-strand	1162-1163	2	29
β-strand	1170-1172	3	29
β-strand	1175-1179	5	28
β-strand	1184-1188	5	28
β-strand	1195	1	28
α-helix	1199-1201	3
β-strand	1202-1204	3	29
β-strand	1213-1214	2	29

Chain B: 40 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	66
β-strand	25-26	2	67
β-strand	35-39	5	68
β-strand	49	1	69
β-strand	54-55	2	57
β-strand	62-68	7	70
α-helix	69	1
β-strand	73-75	3	68
β-strand	76	1	71
β-strand	80	1	72
β-strand	85-86	2	67
α-helix	88-90	3
β-strand	97	1	73
β-strand	101-107	7	71
β-strand	110-113	4	74
β-strand	116-119	4	74
β-strand	123-127	5	73
β-strand	136-141	6	73
β-strand	145	1	75
β-strand	146-151	6	73
β-strand	156	1	66
β-strand	161-162	2	72
β-strand	183-187	5	73
β-strand	190	1	75
β-strand	197-205	9	71
β-strand	208-214	7	71
β-strand	220	1	69
β-strand	221-227	7	71
β-strand	234-238	5	73
β-strand	240-241	2	72
β-strand	256-260	5	71
β-strand	261-270	10	70
β-strand	276-281	6	70
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	76
α-helix	307-309	3
β-strand	317-319	3	77
β-strand	326	1	78
α-helix	329-333	5
β-strand	337-339	3	79
β-strand	346-349	4	80
β-strand	353	1	78
β-strand	354	1	81
α-helix	356-362	7
β-strand	365-371	7	80
α-helix	376-378	3
β-strand	383-392	10	80
α-helix	398-401	4
α-helix	409-413	5
β-strand	422-430	9	80
β-strand	435-437	3	79
α-helix	443-447	5
β-strand	459-462	4	82
β-strand	467-468	2	83
α-helix	479-482	4
β-strand	487	1	84
β-strand	494	1	85
α-helix	495-496	2
β-strand	504-506	3	86
β-strand	515	1	84
β-strand	516-518	3	86
β-strand	522	1	87
β-strand	527	1	87
β-strand	536-537	2	83
β-strand	548	1	83
β-strand	550-551	2	88
α-helix	553-555	3
β-strand	564	1	85
α-helix	569-571	3
β-strand	572-573	2	88
β-strand	576-579	4	82
β-strand	582	1	80
β-strand	585-597	13	80
β-strand	602	1	80
β-strand	604	1	81
β-strand	619-624	6	77
β-strand	627-635	9	77
β-strand	647-649	3	77
β-strand	655-660	6	77
β-strand	665-670	6	77
α-helix	671-673	3
β-strand	678-681	4	76
α-helix	688	1
β-strand	689-693	5	76
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	76
β-strand	718-721	4	76
β-strand	724-731	8	89
β-strand	737	1	89
β-strand	742-746	5	89
β-strand	762-767	6	89
β-strand	773-775	3	27
β-strand	782	1	90
β-strand	785	1	90
β-strand	786-804	19	91
β-strand	809-812	4	92
α-helix	815-819	5
α-helix	826-829	4
α-helix	830-832	3
α-helix	836-861	26
β-strand	866-868	3	59
β-strand	878	1	93
β-strand	883	1	93
α-helix	885-887	3
α-helix	902-909	8
α-helix	915-922	8
α-helix	924-927	4
α-helix	934-940	7
β-strand	943-946	4	92
α-helix	947-948	2
α-helix	952-963	12
α-helix	965-967	3
α-helix	979-988	10
α-helix	994-997	4
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1062	5
α-helix	1067-1069	3
α-helix	1071-1109	39
α-helix	1110-1114	5
β-strand	1129-1137	9	91
β-strand	1140-1158	19	91
β-strand	1159	1	94
β-strand	1162-1163	2	95
β-strand	1169-1172	4	95
β-strand	1175-1179	5	94
β-strand	1184-1188	5	94
β-strand	1195	1	94
β-strand	1202-1205	4	95
β-strand	1213-1214	2	95

Chain C: 38 helices, 89 β-strands

Element	Residues	Length	Sheet
β-strand	35-36	2	36
β-strand	49	1	37
β-strand	55	1	20
β-strand	61-68	8	38
α-helix	69	1
β-strand	75-76	2	36
β-strand	80-81	2	39
α-helix	84-86	3
α-helix	87-90	4
β-strand	96-97	2	40
β-strand	101-107	7	36
β-strand	109-113	5	41
β-strand	116-120	5	41
β-strand	124-127	4	40
β-strand	136-141	6	40
β-strand	145-151	7	40
β-strand	155	1	42
β-strand	161-162	2	39
β-strand	175	1	42
β-strand	183-190	8	40
β-strand	197-205	9	36
β-strand	208-214	7	36
β-strand	220	1	37
β-strand	221-227	7	36
β-strand	234-236	3	40
β-strand	240-241	2	39
β-strand	257-260	4	36
β-strand	261-270	10	38
β-strand	276-281	6	38
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	43
β-strand	309-310	2	44
α-helix	311-313	3
β-strand	316-319	4	45
α-helix	324-325	2
β-strand	326	1	46
α-helix	329-334	6
β-strand	339	1	47
α-helix	341-343	3
β-strand	345-349	5	48
β-strand	353	1	46
β-strand	354	1	49
α-helix	356-362	7
β-strand	368-371	4	48
α-helix	375-377	3
β-strand	383	1	50
β-strand	385-392	8	48
α-helix	399-401	3
α-helix	409-412	4
α-helix	415-417	3
β-strand	422-425	4	48
β-strand	428-430	3	51
β-strand	437	1	47
α-helix	444-447	4
β-strand	460-463	4	52
β-strand	468	1	53
β-strand	477	1	54
α-helix	479-482	4
β-strand	487	1	55
β-strand	492	1	54
α-helix	499-502	4
β-strand	505	1	56
β-strand	515	1	55
β-strand	517	1	56
β-strand	536	1	53
α-helix	569-571	3
β-strand	575-578	4	52
β-strand	581-582	2	51
β-strand	585-587	3	51
β-strand	588-595	8	48
β-strand	602	1	50
β-strand	604	1	49
β-strand	620-624	5	45
β-strand	627-631	5	45
β-strand	632-635	4	57
β-strand	647-649	3	57
β-strand	655-659	5	57
β-strand	666-670	5	57
α-helix	671-673	3
β-strand	674-675	2	44
β-strand	678-681	4	43
α-helix	688	1
β-strand	689-693	5	43
α-helix	697-700	4
β-strand	712-714	3	43
β-strand	718-721	4	43
β-strand	724-731	8	58
β-strand	737-739	3	58
β-strand	742-746	5	58
β-strand	762-767	6	58
β-strand	773-775	3	59
β-strand	786-791	6	60
β-strand	794-804	11	61
β-strand	809-811	3	62
α-helix	814-817	4
α-helix	823-829	7
α-helix	837-861	25
β-strand	866-868	3	22
β-strand	878-879	2	63
β-strand	882-883	2	63
α-helix	902-908	7
α-helix	915-923	9
α-helix	936-939	4
β-strand	944-946	3	62
α-helix	947	1
α-helix	954-964	11
α-helix	979-988	10
α-helix	994-999	6
α-helix	1002-1017	16
α-helix	1018-1020	3
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1062	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	61
β-strand	1140-1150	11	61
β-strand	1153-1158	6	60
β-strand	1159	1	64
β-strand	1162-1163	2	65
β-strand	1169-1172	4	65
β-strand	1175-1179	5	64
β-strand	1184-1188	5	64
β-strand	1195	1	64
β-strand	1202-1205	4	65
β-strand	1213-1214	2	65

Chain T: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	30
α-helix	262-263	2
β-strand	271-275	5	31
β-strand	278-283	6	31
β-strand	284	1	32
β-strand	291-293	3	32
α-helix	300-302	3
α-helix	305-307	3
β-strand	309-312	4	31
β-strand	326-327	2	31
β-strand	328-333	6	32
β-strand	338	1	33
β-strand	343	1	33
β-strand	347-351	5	32
α-helix	365-368	4
β-strand	378-383	6	30
β-strand	398-403	6	30
β-strand	404-405	2	34
α-helix	407-410	4
β-strand	424-427	4	34
β-strand	442	1	34
β-strand	446-447	2	30
β-strand	448-449	2	35
β-strand	452-453	2	35
β-strand	459-461	3	34
β-strand	472-475	4	34
α-helix	481-491	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1263	Human coronavirus HKU1 (isolate N5)	Q0ZME7
Transmembrane protease serine 2	T	protein	383	Homo sapiens	O15393 (AlphaFold model)

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

>8Y87_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

Sequence of entity 2 (T), FASTA

>8Y87_2 Transmembrane protease serine 2 (chains T)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPE
WIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALM
KLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQR
CNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAY
RPGVYGNVMVFTDWIYRQMRADG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	22

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
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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