8Y1F: Spike glycoprotein

The closed conformation of the HKU1-B S protein in the apo state. Determined by electron microscopy at 2.8 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Human coronavirus HKU1 (isolate N2)
Chains: 3
Atoms: 29,541
Mol. weight: 450.02 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1F contains 127 α-helices and 285 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: 44 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
α-helix	32-34	3
β-strand	38-39	2	3
β-strand	49	1	4
β-strand	54-55	2	5
β-strand	59-67	9	6
α-helix	68-69	2
β-strand	73-74	2	3
β-strand	75-76	2	7
β-strand	80-81	2	8
β-strand	85-86	2	2
α-helix	87-90	4
β-strand	96-97	2	9
β-strand	101-107	7	7
β-strand	109-112	4	10
β-strand	117-120	4	10
β-strand	124-127	4	9
β-strand	136-141	6	9
β-strand	145-151	7	9
β-strand	155-160	6	11
β-strand	161-162	2	8
α-helix	171-172	2
β-strand	173-175	3	11
β-strand	183-190	8	9
β-strand	197-205	9	7
β-strand	208-214	7	7
β-strand	220	1	4
β-strand	221-227	7	7
β-strand	234-237	4	9
α-helix	238-239	2
β-strand	240-241	2	8
β-strand	256-260	5	7
β-strand	262-270	9	6
β-strand	276-281	6	6
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	12
β-strand	309-310	2	13
α-helix	311-313	3
β-strand	315-319	5	14
β-strand	326	1	15
α-helix	329-333	5
β-strand	337-339	3	16
β-strand	345-349	5	17
β-strand	353-354	2	15
α-helix	356-362	7
β-strand	364-371	8	17
β-strand	382-383	2	15
β-strand	385-392	8	17
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	17
β-strand	435-437	3	16
α-helix	443-447	5
β-strand	459-463	5	18
β-strand	466-468	3	19
α-helix	476	1
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	495-496	2
α-helix	500-501	2
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	575-579	5	18
β-strand	581-582	2	17
β-strand	585-595	11	17
β-strand	602-604	3	15
β-strand	619-624	6	14
β-strand	627-636	10	14
β-strand	647-649	3	14
β-strand	655-659	5	14
β-strand	666-670	5	14
α-helix	671-673	3
β-strand	674-675	2	13
β-strand	678-681	4	12
β-strand	689-693	5	12
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	12
β-strand	718-721	4	12
β-strand	724-731	8	25
β-strand	737-739	3	25
β-strand	742-746	5	25
β-strand	762-767	6	25
β-strand	773-775	3	26
β-strand	782	1	27
β-strand	785	1	27
β-strand	786-789	4	28
β-strand	793-804	12	29
β-strand	809-812	4	30
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	31
β-strand	878-879	2	32
β-strand	882-883	2	32
α-helix	902-908	7
α-helix	915-922	8
α-helix	934-940	7
β-strand	943-946	4	30
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1016	16
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	29
β-strand	1140-1152	13	29
β-strand	1155-1159	5	28
β-strand	1162-1163	2	33
α-helix	1165-1167	3
β-strand	1169-1172	4	33
β-strand	1175-1179	5	28
β-strand	1184-1188	5	28
β-strand	1195	1	28
β-strand	1202-1205	4	33
β-strand	1213-1214	2	33

Chain B: 42 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	34
β-strand	25-26	2	35
α-helix	31-34	4
β-strand	38-39	2	36
β-strand	49	1	37
β-strand	54-55	2	14
β-strand	59-67	9	38
α-helix	68-69	2
β-strand	73-74	2	36
β-strand	75-76	2	39
β-strand	80-81	2	40
β-strand	85-86	2	35
α-helix	87-90	4
β-strand	96-97	2	41
β-strand	101-107	7	39
β-strand	109-112	4	42
β-strand	117-120	4	42
β-strand	124-127	4	41
β-strand	136-141	6	41
β-strand	145-151	7	41
β-strand	155-160	6	43
β-strand	161-162	2	40
β-strand	167	1	44
α-helix	171-172	2
β-strand	173-175	3	43
β-strand	183-190	8	41
β-strand	197-205	9	39
β-strand	208-214	7	39
β-strand	220	1	37
β-strand	221-227	7	39
β-strand	234-237	4	41
β-strand	240-241	2	40
β-strand	242	1	44
β-strand	256-260	5	39
β-strand	262-270	9	38
β-strand	276-281	6	38
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	45
β-strand	309-310	2	46
α-helix	311-313	3
β-strand	315-319	5	47
β-strand	326	1	48
α-helix	329-333	5
β-strand	337-339	3	49
β-strand	345-349	5	48
β-strand	353-354	2	48
α-helix	356-362	7
β-strand	364-371	8	48
α-helix	375-378	4
β-strand	382-392	11	48
α-helix	393-394	2
α-helix	395-401	7
α-helix	408	1
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	48
β-strand	435-437	3	49
α-helix	443-447	5
β-strand	459-463	5	50
β-strand	466-468	3	51
β-strand	477	1	52
α-helix	478	1
α-helix	481-484	4
β-strand	492	1	52
β-strand	494	1	53
α-helix	495-496	2
α-helix	500-501	2
β-strand	502	1	52
β-strand	504-507	4	54
β-strand	515-518	4	54
β-strand	536-538	3	51
β-strand	550-551	2	55
α-helix	553-555	3
β-strand	556	1	56
β-strand	558	1	52
β-strand	564	1	53
β-strand	567	1	56
α-helix	569-571	3
β-strand	572-573	2	55
β-strand	575-579	5	50
β-strand	581-582	2	48
β-strand	585-597	13	48
β-strand	602-604	3	48
β-strand	619-624	6	47
β-strand	627-636	10	47
β-strand	647-649	3	47
β-strand	655-659	5	47
β-strand	666-670	5	47
α-helix	671-673	3
β-strand	674-675	2	46
β-strand	678-681	4	45
β-strand	689-693	5	45
α-helix	697-703	7
β-strand	712-714	3	45
β-strand	718-721	4	45
β-strand	724-731	8	57
β-strand	737-739	3	57
β-strand	742-746	5	57
β-strand	762-767	6	57
β-strand	773-775	3	58
β-strand	782	1	59
β-strand	785	1	59
β-strand	786-804	19	60
β-strand	809-812	4	61
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	26
β-strand	878-879	2	62
β-strand	882-883	2	62
α-helix	902-908	7
α-helix	915-922	8
α-helix	934-940	7
β-strand	943-946	4	61
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1016	16
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	60
β-strand	1140-1158	19	60
β-strand	1159	1	63
β-strand	1162-1163	2	64
β-strand	1169-1172	4	64
β-strand	1175-1179	5	63
β-strand	1184-1188	5	63
β-strand	1195	1	63
β-strand	1202-1205	4	64
α-helix	1212	1
β-strand	1213-1214	2	64

Chain C: 41 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	65
β-strand	25-26	2	66
α-helix	32-34	3
β-strand	38-39	2	67
β-strand	49	1	68
β-strand	54-55	2	47
β-strand	59-67	9	69
α-helix	68-69	2
β-strand	73-74	2	67
β-strand	76	1	70
β-strand	80-81	2	71
β-strand	85-86	2	66
α-helix	88-90	3
β-strand	96-97	2	72
β-strand	101-107	7	70
β-strand	109-113	5	73
β-strand	116-120	5	73
β-strand	124-127	4	72
β-strand	136-141	6	72
β-strand	145-151	7	72
β-strand	155-160	6	74
β-strand	161-162	2	71
β-strand	167	1	75
α-helix	171-172	2
β-strand	173-175	3	74
β-strand	183-190	8	72
β-strand	197-205	9	70
β-strand	208-214	7	70
β-strand	220	1	68
β-strand	221-227	7	70
β-strand	234-237	4	72
β-strand	240-241	2	71
β-strand	242	1	75
β-strand	256-260	5	70
β-strand	262-270	9	69
β-strand	276-281	6	69
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	76
β-strand	309-310	2	77
α-helix	311-313	3
β-strand	315-319	5	5
β-strand	326	1	78
α-helix	329-333	5
β-strand	337-339	3	79
β-strand	345-349	5	78
β-strand	353-354	2	78
α-helix	356-362	7
β-strand	364-371	8	78
α-helix	375-377	3
β-strand	382-392	11	78
α-helix	395-401	7
α-helix	408	1
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	78
β-strand	435-437	3	79
α-helix	443-446	4
β-strand	459-463	5	80
β-strand	466-468	3	81
β-strand	477	1	82
α-helix	482-484	3
β-strand	487	1	83
β-strand	492	1	82
β-strand	494	1	84
α-helix	495-496	2
β-strand	502	1	82
β-strand	504-507	4	83
β-strand	515-518	4	83
β-strand	536-538	3	81
β-strand	550-551	2	85
α-helix	553-555	3
β-strand	556	1	86
β-strand	558	1	82
β-strand	564	1	84
β-strand	567	1	86
α-helix	569-571	3
β-strand	572-573	2	85
β-strand	575-579	5	80
β-strand	581	1	78
β-strand	585-597	13	78
β-strand	602-604	3	78
α-helix	610-613	4
β-strand	619-624	6	5
β-strand	627-636	10	5
β-strand	647-649	3	5
β-strand	655-659	5	5
β-strand	666-670	5	5
α-helix	671-673	3
β-strand	674-675	2	77
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	87
β-strand	737-739	3	87
β-strand	742-746	5	87
β-strand	762-767	6	87
β-strand	773-775	3	31
β-strand	782	1	88
β-strand	785	1	88
β-strand	786-804	19	89
β-strand	809-812	4	90
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	58
β-strand	878-879	2	91
β-strand	882-883	2	91
α-helix	902-908	7
α-helix	915-922	8
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	1001-1016	16
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	89
β-strand	1140-1159	20	89
β-strand	1162-1163	2	92
β-strand	1169-1172	4	92
β-strand	1175-1179	5	89
β-strand	1184-1188	5	89
β-strand	1195	1	89
β-strand	1202-1205	4	92
β-strand	1213-1214	2	92

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

>8Y1F_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
8Y1G 2.99 Å, The 1up conformation of the HKU1-B S protein in the apo state
8Y1H 3.16 Å, The 2up formation of the HKU1-B S protein in the apo state

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