8Y88: Spike glycoprotein

Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2. Determined by electron microscopy at 3.03 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Human coronavirus HKU1, Homo sapiens
Chains: 5
Atoms: 31,257
Mol. weight: 511.14 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y88 contains 116 α-helices and 318 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: 32 helices, 81 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	1
β-strand	54-55	2	2
β-strand	60-67	8	3
α-helix	68-69	2
β-strand	75	1	1
β-strand	76	1	4
β-strand	80-81	2	5
β-strand	96-97	2	6
β-strand	101-107	7	4
β-strand	110-111	2	7
α-helix	113-115	3
β-strand	118-119	2	7
β-strand	124-127	4	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	185-189	5	6
β-strand	197-205	9	4
β-strand	208-214	7	4
β-strand	221-226	6	4
β-strand	234-236	3	6
β-strand	240-241	2	5
β-strand	256-260	5	4
β-strand	262-270	9	3
β-strand	276-281	6	3
α-helix	286-294	9
β-strand	302-305	4	9
β-strand	310	1	10
α-helix	311-313	3
β-strand	316-319	4	11
β-strand	326	1	12
α-helix	341-343	3
β-strand	346-348	3	13
β-strand	353-354	2	12
α-helix	356-362	7
β-strand	365-368	4	13
β-strand	371	1	13
α-helix	375-377	3
β-strand	383-390	8	13
α-helix	398-401	4
α-helix	409-412	4
α-helix	415-417	3
β-strand	422-430	9	13
α-helix	444-447	4
β-strand	461-463	3	14
β-strand	467-468	2	15
α-helix	489-491	3
β-strand	536-537	2	15
β-strand	551	1	16
β-strand	556-557	2	17
β-strand	566-567	2	17
β-strand	572	1	16
β-strand	575-577	3	14
β-strand	582	1	13
β-strand	585-597	13	13
β-strand	602	1	13
β-strand	603-604	2	12
α-helix	612-614	3
β-strand	620-624	5	11
β-strand	627-631	5	11
β-strand	632-636	5	18
β-strand	647-649	3	18
β-strand	655-659	5	18
β-strand	666-670	5	18
β-strand	674	1	10
β-strand	678-681	4	9
α-helix	688	1
β-strand	689-693	5	9
α-helix	697-703	7
β-strand	712-714	3	9
β-strand	718-721	4	9
β-strand	724-731	8	19
β-strand	737	1	19
β-strand	742-745	4	19
β-strand	763-767	5	19
β-strand	773-775	3	20
β-strand	786-791	6	21
β-strand	794-803	10	22
β-strand	809-812	4	23
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	24
β-strand	878-879	2	25
β-strand	882-883	2	25
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	935-941	7
β-strand	943-946	4	23
α-helix	952-965	14
α-helix	979-989	11
α-helix	994-997	4
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1064	7
α-helix	1071-1109	39
α-helix	1110-1114	5
β-strand	1132-1137	6	22
β-strand	1140-1150	11	22
β-strand	1153-1158	6	21
β-strand	1159	1	26
β-strand	1162-1163	2	27
β-strand	1169-1172	4	28
β-strand	1175-1179	5	26
β-strand	1184-1188	5	26
β-strand	1195	1	26
β-strand	1202-1205	4	28
β-strand	1213-1214	2	27

Chain B: 40 helices, 100 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	62
α-helix	32-34	3
β-strand	35-39	5	63
α-helix	40	1
β-strand	49	1	64
β-strand	60	1	65
β-strand	63-67	5	66
α-helix	68-69	2
β-strand	73-76	4	63
β-strand	80	1	67
β-strand	85	1	62
α-helix	88-90	3
β-strand	96-97	2	68
β-strand	101-107	7	63
β-strand	109-113	5	69
β-strand	116-120	5	69
β-strand	123-127	5	68
β-strand	136-141	6	68
β-strand	145-151	7	68
β-strand	155	1	70
β-strand	161-162	2	67
β-strand	175	1	70
α-helix	180-182	3
β-strand	183-190	8	68
β-strand	197-205	9	63
β-strand	208-214	7	63
β-strand	220	1	64
β-strand	221-227	7	63
β-strand	234-238	5	68
β-strand	240-241	2	67
β-strand	256-260	5	63
β-strand	262-266	5	66
β-strand	269	1	65
β-strand	270	1	71
β-strand	276	1	71
β-strand	281	1	66
α-helix	286-294	9
β-strand	302-305	4	72
α-helix	307-309	3
β-strand	317-319	3	73
β-strand	326	1	74
α-helix	329-333	5
β-strand	337-339	3	75
β-strand	346-350	5	76
β-strand	353	1	74
β-strand	354	1	77
α-helix	356-362	7
β-strand	365-371	7	76
β-strand	382-383	2	78
β-strand	385-392	8	76
α-helix	398-401	4
α-helix	409-412	4
β-strand	415	1	79
α-helix	416-417	2
β-strand	422-430	9	76
β-strand	435-437	3	75
α-helix	446-448	3
β-strand	459-463	5	80
β-strand	467-468	2	81
α-helix	482-484	3
β-strand	487	1	82
β-strand	494	1	83
α-helix	495-496	2
β-strand	504-506	3	84
β-strand	515	1	82
β-strand	516-518	3	84
β-strand	522	1	85
β-strand	527	1	85
β-strand	536-537	2	81
β-strand	542	1	79
β-strand	550-551	2	86
α-helix	553-555	3
β-strand	564	1	83
α-helix	569-571	3
β-strand	572-573	2	86
β-strand	575-579	5	80
β-strand	581-582	2	76
β-strand	585-595	11	76
β-strand	602-603	2	78
β-strand	604	1	77
β-strand	619-624	6	73
β-strand	627-632	6	73
β-strand	635	1	2
β-strand	647-649	3	2
β-strand	655-660	6	2
β-strand	665-667	3	2
β-strand	670	1	73
α-helix	671-673	3
β-strand	678-681	4	72
α-helix	688	1
β-strand	689-693	5	72
α-helix	700-704	5
β-strand	712-714	3	72
β-strand	718-721	4	72
β-strand	730-731	2	87
β-strand	737-739	3	87
β-strand	742-743	2	87
α-helix	746-748	3
β-strand	765-767	3	87
β-strand	773-775	3	24
β-strand	782	1	88
β-strand	785	1	88
β-strand	786-791	6	89
β-strand	794-795	2	90
β-strand	798-803	6	91
β-strand	809-812	4	92
α-helix	823-829	7
α-helix	830-832	3
α-helix	837-862	26
β-strand	866-868	3	55
β-strand	878	1	93
β-strand	883	1	93
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-922	8
α-helix	932-933	2
α-helix	934-939	6
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	994-999	6
α-helix	1001-1017	17
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	91
β-strand	1140-1147	8	91
β-strand	1149-1150	2	90
β-strand	1153-1159	7	89
β-strand	1162-1163	2	94
β-strand	1169-1172	4	94
β-strand	1175-1179	5	89
β-strand	1184-1188	5	89
β-strand	1195	1	89
β-strand	1202-1204	3	94
β-strand	1213-1214	2	94

Chain C: 33 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	29
β-strand	39	1	30
β-strand	49	1	31
α-helix	50-51	2
β-strand	60-67	8	32
α-helix	68-69	2
β-strand	73	1	30
β-strand	75-76	2	33
β-strand	85	1	29
α-helix	87-90	4
β-strand	96-97	2	34
β-strand	101-107	7	33
β-strand	110-112	3	35
β-strand	117-119	3	35
β-strand	124-127	4	34
β-strand	136-141	6	34
β-strand	145-149	5	34
β-strand	155-160	6	36
β-strand	161	1	37
β-strand	173-175	3	36
β-strand	186-190	5	34
β-strand	197-205	9	33
β-strand	208-214	7	33
β-strand	220	1	31
β-strand	221-227	7	33
β-strand	234-237	4	34
β-strand	240	1	37
β-strand	256-260	5	33
β-strand	262-270	9	32
β-strand	276-281	6	32
α-helix	286-294	9
β-strand	302-305	4	38
β-strand	309-310	2	39
β-strand	316	1	40
α-helix	325-326	2
α-helix	330-334	5
β-strand	337-338	2	41
β-strand	346-349	4	42
β-strand	354	1	43
α-helix	356-359	4
β-strand	364-370	7	42
α-helix	375-378	4
β-strand	382-383	2	44
β-strand	385-392	8	42
α-helix	409-412	4
β-strand	423-430	8	42
β-strand	435-436	2	41
β-strand	459-463	5	45
β-strand	467-468	2	46
β-strand	477	1	47
α-helix	479-482	4
β-strand	487	1	48
β-strand	492	1	47
β-strand	494	1	49
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-506	3	50
β-strand	515	1	48
β-strand	516-518	3	50
β-strand	522	1	51
β-strand	527	1	51
β-strand	536-537	2	46
β-strand	548	1	46
β-strand	550-551	2	52
α-helix	553-555	3
β-strand	564	1	49
α-helix	569-571	3
β-strand	572-573	2	52
β-strand	575-579	5	45
β-strand	581	1	42
β-strand	585-595	11	42
β-strand	602-603	2	44
β-strand	604	1	43
α-helix	612-615	4
β-strand	619-620	2	53
β-strand	621	1	40
β-strand	631-635	5	53
β-strand	647-648	2	53
β-strand	657-659	3	53
β-strand	666-670	5	53
α-helix	671-673	3
β-strand	674-675	2	39
β-strand	678-681	4	38
α-helix	688	1
β-strand	689-693	5	38
α-helix	697-703	7
β-strand	712-714	3	38
β-strand	718-721	4	38
β-strand	724-731	8	54
β-strand	736-739	4	54
β-strand	742-746	5	54
β-strand	762-767	6	54
β-strand	773-775	3	55
β-strand	782	1	56
β-strand	785	1	56
β-strand	786-803	18	57
β-strand	809-811	3	58
α-helix	823-830	8
α-helix	835-861	27
β-strand	866-868	3	20
β-strand	878	1	59
β-strand	883	1	59
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	936-939	4
β-strand	944-946	3	58
α-helix	954-964	11
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1017	17
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1058-1062	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	57
β-strand	1140-1158	19	57
β-strand	1159	1	60
β-strand	1162-1164	3	61
β-strand	1168-1172	5	61
β-strand	1175-1179	5	60
β-strand	1184-1188	5	60
β-strand	1195	1	60
β-strand	1202-1205	4	61
β-strand	1213-1214	2	61

Chain I: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	102
α-helix	262-263	2
β-strand	271-275	5	103
β-strand	278-283	6	103
β-strand	284	1	104
β-strand	291-293	3	104
α-helix	300-302	3
β-strand	309-311	3	103
β-strand	326-327	2	103
β-strand	328-333	6	104
β-strand	338	1	105
β-strand	343	1	105
β-strand	347-351	5	104
β-strand	365	1	106
α-helix	366-368	3
β-strand	378-383	6	102
β-strand	398-403	6	102
β-strand	404-405	2	107
α-helix	407-410	4
β-strand	424-427	4	107
β-strand	442-445	4	107
β-strand	446-447	2	102
β-strand	448-449	2	108
β-strand	452-453	2	108
β-strand	454	1	106
β-strand	457-459	3	107
β-strand	472-475	4	107
α-helix	481-491	11

Chain T: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	95
α-helix	262-263	2
β-strand	271-275	5	96
β-strand	278-283	6	96
β-strand	284	1	97
β-strand	291-293	3	97
α-helix	300-302	3
β-strand	309-311	3	96
β-strand	326-327	2	96
β-strand	328-333	6	97
β-strand	338	1	98
β-strand	343	1	98
β-strand	347-351	5	97
α-helix	365-368	4
β-strand	378-383	6	95
β-strand	398-403	6	95
β-strand	404-405	2	99
α-helix	406	1
α-helix	407-410	4
β-strand	424-427	4	99
β-strand	442-445	4	100
β-strand	446-447	2	95
β-strand	448-449	2	101
β-strand	452-453	2	101
β-strand	457-459	3	100
β-strand	472-475	4	99
α-helix	481-491	11

Molecules and chains

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

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

>8Y88_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 (I, T), FASTA

>8Y88_2 Transmembrane protease serine 2 (chains I, 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	18

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
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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