8Y1H: Spike glycoprotein

The 2up formation of the HKU1-B S protein in the apo state. Determined by electron microscopy at 3.16 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 3.16 Å
Organism: Human coronavirus HKU1 (isolate N2)
Chains: 3
Atoms: 29,541
Mol. weight: 450.02 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1H contains 107 α-helices and 296 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: 33 helices, 97 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	76
β-strand	49	1	77
β-strand	54-56	3	62
β-strand	60-61	2	78
β-strand	64-68	5	79
α-helix	69	1
β-strand	76	1	80
β-strand	80-81	2	81
α-helix	87-90	4
β-strand	96-97	2	82
β-strand	102-107	6	80
β-strand	110-111	2	83
β-strand	118-119	2	83
β-strand	124-127	4	82
β-strand	136-141	6	82
β-strand	145-151	7	82
β-strand	155	1	84
β-strand	156	1	76
β-strand	161-162	2	81
β-strand	175	1	84
β-strand	186-190	5	82
β-strand	197-205	9	80
β-strand	208-214	7	80
β-strand	220	1	77
β-strand	221-222	2	80
β-strand	227	1	80
β-strand	234-237	4	82
β-strand	240-241	2	81
β-strand	256-257	2	80
β-strand	261-265	5	79
β-strand	266-270	5	78
β-strand	276-281	6	78
α-helix	287-294	8
β-strand	302-307	6	85
β-strand	337-338	2	86
β-strand	345-349	5	87
β-strand	354	1	88
α-helix	357-361	5
β-strand	367-371	5	87
α-helix	375-380	6
β-strand	383	1	89
β-strand	385-392	8	87
α-helix	393-394	2
α-helix	395-400	6
β-strand	421-430	10	87
β-strand	435-436	2	86
α-helix	443-446	4
β-strand	459-463	5	90
β-strand	467-468	2	91
β-strand	477	1	92
β-strand	492	1	92
β-strand	494	1	93
α-helix	495-496	2
α-helix	501	1
β-strand	502	1	92
α-helix	503	1
β-strand	504-507	4	94
β-strand	515-518	4	94
α-helix	530-532	3
β-strand	536-537	2	91
α-helix	549	1
β-strand	550-551	2	95
α-helix	552	1
β-strand	556	1	96
β-strand	564	1	93
β-strand	567	1	96
β-strand	572-573	2	95
β-strand	575-579	5	90
β-strand	581	1	87
β-strand	585-595	11	87
β-strand	602	1	89
β-strand	604	1	88
β-strand	616	1	3
β-strand	619-624	6	3
β-strand	627-636	10	3
β-strand	642	1	97
β-strand	645	1	97
β-strand	647-649	3	3
β-strand	655-659	5	3
β-strand	666-671	6	3
β-strand	676-681	6	85
α-helix	688	1
β-strand	689	1	85
β-strand	690-693	4	98
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	98
β-strand	718-721	4	98
β-strand	724-731	8	99
β-strand	737	1	99
β-strand	742-746	5	99
β-strand	762-767	6	99
β-strand	773-775	3	32
β-strand	782	1	100
β-strand	785	1	100
β-strand	786-790	5	101
β-strand	794-803	10	102
β-strand	809-812	4	103
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	835-862	28
β-strand	866-868	3	64
β-strand	878-879	2	104
β-strand	882-883	2	104
α-helix	902-910	9
α-helix	915-923	9
α-helix	935-939	5
β-strand	943-946	4	103
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	995-1016	22
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1069-1109	41
α-helix	1110-1114	5
β-strand	1129-1133	5	102
β-strand	1141-1150	10	102
β-strand	1154-1158	5	101
β-strand	1159	1	105
β-strand	1162-1164	3	106
β-strand	1168-1171	4	106
β-strand	1176-1177	2	105
β-strand	1180	1	107
β-strand	1183	1	107
β-strand	1186-1187	2	105
β-strand	1203-1204	2	106
β-strand	1213-1214	2	106

Chain B: 35 helices, 94 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	1
β-strand	46	1	2
β-strand	48	1	2
β-strand	54-55	2	3
β-strand	60-61	2	4
β-strand	65-66	2	5
β-strand	75	1	1
β-strand	79-81	3	6
α-helix	87-90	4
β-strand	96-97	2	7
β-strand	103-107	5	8
β-strand	109-111	3	9
β-strand	118-120	3	9
β-strand	124-127	4	7
β-strand	136-141	6	7
β-strand	145	1	10
β-strand	146-151	6	7
β-strand	155-160	6	11
β-strand	161	1	6
β-strand	173-175	3	11
β-strand	183-187	5	7
β-strand	190	1	10
β-strand	197-201	5	8
β-strand	204-205	2	12
β-strand	208-213	6	12
α-helix	220	1
β-strand	221-227	7	12
β-strand	234-236	3	7
α-helix	237-238	2
β-strand	239-241	3	6
β-strand	257-259	3	8
β-strand	263-264	2	5
β-strand	267-270	4	4
β-strand	276-280	5	4
α-helix	286-294	9
β-strand	302-307	6	13
β-strand	318-319	2	14
β-strand	337-339	3	15
α-helix	340	1
β-strand	347-349	3	16
α-helix	356-362	7
β-strand	364-369	6	16
α-helix	375-378	4
β-strand	382-383	2	17
β-strand	385-392	8	16
α-helix	393-394	2
α-helix	409-413	5
β-strand	423-430	8	16
β-strand	435-437	3	15
α-helix	443-447	5
β-strand	460-463	4	18
β-strand	466-468	3	19
β-strand	477	1	20
α-helix	478	1
α-helix	482-484	3
β-strand	492	1	20
β-strand	494	1	21
α-helix	499-501	3
β-strand	502	1	20
α-helix	503	1
β-strand	504-507	4	22
β-strand	515-518	4	22
β-strand	536-538	3	19
β-strand	550-551	2	23
α-helix	553-555	3
β-strand	556	1	24
β-strand	558	1	20
β-strand	564	1	21
β-strand	567	1	24
α-helix	569-571	3
β-strand	572-573	2	23
β-strand	575-578	4	18
β-strand	581	1	16
β-strand	585-595	11	16
β-strand	602-603	2	17
β-strand	620-624	5	14
β-strand	627-636	10	14
β-strand	647-649	3	14
β-strand	655-659	5	14
β-strand	666-671	6	14
α-helix	672-673	2
β-strand	676-681	6	13
β-strand	689-691	3	13
α-helix	697-702	6
β-strand	712-714	3	13
β-strand	719-721	3	13
β-strand	724-731	8	25
β-strand	737	1	25
β-strand	742-745	4	25
β-strand	763-767	5	25
α-helix	772	1
β-strand	773-775	3	26
β-strand	782	1	27
β-strand	785	1	27
β-strand	786-791	6	28
β-strand	794-797	4	29
β-strand	800-803	4	30
β-strand	809-812	4	31
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-862	27
β-strand	866-868	3	32
β-strand	878	1	33
β-strand	883	1	33
α-helix	902-907	6
α-helix	917-922	6
α-helix	923-925	3
α-helix	935-939	5
β-strand	943-946	4	31
α-helix	952-964	13
α-helix	979-988	10
α-helix	995-999	5
α-helix	1001-1016	16
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	1129-1131	3	29
β-strand	1134-1137	4	30
β-strand	1140-1144	5	30
β-strand	1146-1150	5	29
β-strand	1153-1159	7	28
β-strand	1162-1164	3	34
β-strand	1168-1172	5	34
β-strand	1177-1179	3	28
β-strand	1184-1186	3	28
β-strand	1195	1	28
β-strand	1202-1205	4	34

Chain C: 39 helices, 105 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	35
β-strand	49	1	36
β-strand	54-56	3	14
β-strand	64-67	4	37
α-helix	68-69	2
β-strand	70	1	38
β-strand	72	1	38
β-strand	75-76	2	35
β-strand	80	1	39
α-helix	87-89	3
α-helix	92-94	3
β-strand	101-107	7	35
β-strand	109-112	4	40
β-strand	117-120	4	40
β-strand	123-127	5	41
β-strand	137-141	5	41
β-strand	145-151	7	41
α-helix	153-154	2
β-strand	155	1	42
β-strand	161	1	39
β-strand	175	1	42
β-strand	183-190	8	41
β-strand	201-203	3	35
β-strand	204-205	2	43
β-strand	208-209	2	43
β-strand	212-213	2	44
β-strand	220	1	36
β-strand	221-222	2	44
β-strand	227	1	43
β-strand	234-238	5	41
α-helix	239	1
β-strand	240	1	39
β-strand	255-260	6	35
β-strand	262-265	4	37
β-strand	266-267	2	45
β-strand	270	1	46
β-strand	276	1	46
β-strand	280-281	2	45
α-helix	288-294	7
α-helix	299-300	2
β-strand	302-306	5	47
β-strand	319	1	48
β-strand	326	1	49
α-helix	329-333	5
β-strand	337-339	3	50
β-strand	345-348	4	51
β-strand	353-354	2	49
α-helix	356-361	6
β-strand	364-371	8	51
α-helix	375-377	3
β-strand	385-392	8	51
α-helix	393-394	2
α-helix	395-401	7
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	51
β-strand	435-437	3	50
α-helix	443-446	4
β-strand	460-462	3	52
β-strand	466	1	53
β-strand	467-468	2	54
β-strand	473	1	55
β-strand	477	1	56
α-helix	489-491	3
β-strand	492	1	56
β-strand	494	1	57
α-helix	495-496	2
β-strand	500	1	55
β-strand	505-507	3	58
β-strand	515-517	3	58
β-strand	522	1	59
β-strand	527	1	59
β-strand	536-537	2	54
α-helix	540-541	2
β-strand	549	1	53
α-helix	553-555	3
β-strand	556	1	60
β-strand	564	1	57
β-strand	567	1	60
β-strand	576-578	3	52
β-strand	581-582	2	51
β-strand	585-595	11	51
β-strand	603-604	2	49
β-strand	620-621	2	61
β-strand	624	1	48
β-strand	627	1	48
β-strand	630-631	2	61
β-strand	632-635	4	62
β-strand	647-649	3	62
β-strand	655-659	5	62
β-strand	666-670	5	62
α-helix	671-674	4
β-strand	677-681	5	47
β-strand	690-693	4	47
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	47
β-strand	718-721	4	47
β-strand	724-731	8	63
β-strand	737	1	63
β-strand	743-746	4	63
β-strand	762-767	6	63
β-strand	773-775	3	64
β-strand	786-791	6	65
β-strand	794-796	3	66
β-strand	799-804	6	67
β-strand	809-812	4	68
α-helix	814-818	5
α-helix	823-829	7
α-helix	835-861	27
β-strand	866-868	3	26
β-strand	878-879	2	69
β-strand	882-883	2	69
α-helix	903-910	8
α-helix	915-923	9
α-helix	934-941	8
β-strand	943-946	4	68
α-helix	947-948	2
α-helix	953-964	12
α-helix	972-974	3
α-helix	979-989	11
α-helix	994-999	6
α-helix	1001-1016	16
α-helix	1024-1045	22
α-helix	1058-1061	4
α-helix	1070-1109	40
α-helix	1110-1114	5
β-strand	1129-1131	3	70
β-strand	1137	1	67
β-strand	1140-1145	6	67
β-strand	1146-1147	2	70
β-strand	1148-1150	3	66
β-strand	1153-1158	6	65
β-strand	1164	1	71
β-strand	1168	1	71
β-strand	1169	1	72
β-strand	1172	1	73
β-strand	1176	1	74
β-strand	1179-1180	2	75
β-strand	1183-1184	2	75
β-strand	1187	1	74
α-helix	1199-1201	3
β-strand	1202	1	73
β-strand	1205	1	72

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1290	Human coronavirus HKU1 (isolate N2)	Q14EB0

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

>8Y1H_1 Spike glycoprotein (chains A, B, C)
MFLIIFILPTTLAVIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTT
LLFTGYFPKSGANFRDLALKGSKYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSE
FSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSE
PLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPL
TCKAISSNTDNETLEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPN
TGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLL
RLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISS
SSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNVSSYDVVYSDHCFSVNSDFCPCADPS
VVNSCVKSKPLSAICPAGTKYRHCDLDTTLYVNNWCRCSCLPDPISTYSPNTCPQKKVVV
GIGEHCPGLGINEEKCGTQLNHSSCSCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSG
TTCSNDLLYSNTEVSTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKD
FLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCV
LNAVNLTSYSVSSCDLRMGSGFCIDYALPSSGSASRGISSPYRFVTFEPFNVSFVNDSVE
TVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNIN
SILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSR
SLLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTT
AATVAAMFPPWSAAAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFT
ATNSALAKIQSVVNANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLING
RLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYG
LLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDK
NVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAEFSLWFKNHTSIAPNLTFNSHINATFLD
LYYEMNVIQESIKSLNSSFINLKEIGTYEM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	51

Primary citation

Structural basis for the recognition of HCoV-HKU1 by human TMPRSS2. Xia, L., Zhang, Y., Zhou, Q. Cell Res (2024) 34:526-529. DOI 10.1038/s41422-024-00958-9 · PubMed

Other PDB entries of the same protein (UniProt Q14EB0), best resolution first:

8Y19 2.3 Å, Closed conformation of HKU1-B S protein after incubation of the receptor
8Y1D 2.7 Å, 2up-TM conformation of HKU1-B S protein after incubation of the receptor
8Y1E 2.7 Å, 3up-TM conformation of HKU1-B S protein after incubation of the receptor
8Y1A 2.8 Å, 1up-1 conformation of HKU1-B S protein after incubation of the receptor
8Y1B 2.8 Å, 1up-2 conformation of HKU1-B S protein after incubation of the receptor
8Y1C 2.8 Å, 2up-1 conformation of HKU1-B S protein after incubation of the receptor
8Y1F 2.8 Å, The closed conformation of the HKU1-B S protein in the apo state
8Y1G 2.99 Å, The 1up conformation of the HKU1-B S protein in the apo state

Browse structure collections

About this viewer

MolViewer shows 8Y1H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.