8Y1C: Spike glycoprotein

2up-1 conformation of HKU1-B S protein after incubation of the receptor. 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 8Y1C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1C contains 104 α-helices and 270 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, 94 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	58
β-strand	25	1	59
α-helix	32-34	3
α-helix	42-44	3
β-strand	49	1	60
β-strand	54-55	2	37
β-strand	59-67	9	61
β-strand	76	1	62
β-strand	80-81	2	63
β-strand	85	1	59
α-helix	87-90	4
β-strand	97	1	64
β-strand	101-107	7	62
β-strand	109-112	4	65
β-strand	117-120	4	65
β-strand	124-127	4	64
β-strand	136-141	6	64
β-strand	145-151	7	64
β-strand	155	1	66
β-strand	156	1	58
β-strand	161-162	2	63
β-strand	175	1	66
β-strand	183-190	8	64
β-strand	197-205	9	62
β-strand	208-214	7	62
β-strand	220	1	60
β-strand	221-227	7	62
β-strand	234-237	4	64
β-strand	240-241	2	63
β-strand	256-260	5	62
β-strand	262-270	9	61
β-strand	276-281	6	61
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	67
β-strand	316	1	4
β-strand	319	1	4
α-helix	329-332	4
β-strand	337-338	2	68
β-strand	345-349	5	69
β-strand	354	1	70
α-helix	357-362	6
β-strand	364-371	8	69
α-helix	375-378	4
β-strand	382-383	2	71
β-strand	385-392	8	69
α-helix	398-400	3
β-strand	415	1	72
β-strand	422-430	9	69
β-strand	435-436	2	68
α-helix	443-446	4
β-strand	459-463	5	73
β-strand	467-468	2	74
β-strand	473-477	5	75
α-helix	478	1
β-strand	492	1	75
β-strand	494	1	76
α-helix	495-496	2
β-strand	500-502	3	75
β-strand	505-507	3	77
β-strand	515-517	3	77
β-strand	536-537	2	74
α-helix	538-540	3
β-strand	542	1	72
β-strand	550-551	2	78
β-strand	558	1	75
β-strand	564	1	76
α-helix	569-571	3
β-strand	572-573	2	78
β-strand	575-579	5	73
β-strand	585-595	11	69
β-strand	602-603	2	71
β-strand	604	1	70
β-strand	616	1	4
β-strand	619-624	6	4
β-strand	627-636	10	4
β-strand	647-649	3	4
β-strand	655-659	5	4
β-strand	666-670	5	4
α-helix	671-673	3
β-strand	677-681	5	67
β-strand	689-693	5	67
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	67
β-strand	718-721	4	67
β-strand	724-731	8	79
β-strand	736-739	4	79
β-strand	742-746	5	79
β-strand	762-767	6	79
β-strand	773-775	3	26
β-strand	782	1	80
β-strand	785	1	80
β-strand	786-804	19	81
β-strand	809-812	4	82
α-helix	814-818	5
α-helix	823-829	7
α-helix	835-862	28
β-strand	866-868	3	52
β-strand	878-879	2	83
β-strand	882-883	2	83
α-helix	902-909	8
α-helix	915-922	8
α-helix	934-940	7
β-strand	943-946	4	82
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	1025-1044	20
α-helix	1045-1048	4
α-helix	1058-1061	4
α-helix	1070-1109	40
α-helix	1110-1114	5
β-strand	1125	1	84
β-strand	1127	1	84
β-strand	1129-1137	9	81
β-strand	1140-1158	19	81
β-strand	1159	1	85
β-strand	1162-1164	3	86
β-strand	1168-1172	5	86
β-strand	1175-1180	6	85
β-strand	1183-1188	6	85
β-strand	1195	1	85
β-strand	1202-1205	4	86
β-strand	1213-1214	2	86

Chain B: 34 helices, 85 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	1
β-strand	46	1	2
β-strand	48	1	2
β-strand	49	1	3
β-strand	54-55	2	4
β-strand	59-68	10	5
β-strand	75	1	1
β-strand	80-81	2	6
α-helix	87-89	3
β-strand	96	1	7
β-strand	101-107	7	8
β-strand	109-112	4	9
β-strand	117-120	4	9
β-strand	124-127	4	7
β-strand	136-141	6	7
β-strand	145-151	7	7
β-strand	155-160	6	10
β-strand	161	1	6
β-strand	173-175	3	10
β-strand	185-190	6	7
β-strand	197-205	9	8
β-strand	208-214	7	8
β-strand	220	1	3
β-strand	221-227	7	8
β-strand	234-236	3	7
β-strand	240-241	2	6
β-strand	256-259	4	8
β-strand	261-270	10	5
β-strand	276-281	6	5
α-helix	286-294	9
β-strand	302-306	5	11
β-strand	318-319	2	12
α-helix	330-333	4
β-strand	337-339	3	13
α-helix	340	1
β-strand	345-349	5	14
β-strand	353-354	2	14
α-helix	356-362	7
β-strand	364-369	6	14
α-helix	375-377	3
β-strand	382-392	11	14
α-helix	399-401	3
α-helix	408-412	5
β-strand	422-430	9	14
β-strand	435-437	3	13
α-helix	443-446	4
β-strand	459-463	5	15
β-strand	466-468	3	16
β-strand	477	1	17
α-helix	479-482	4
β-strand	492	1	17
β-strand	494	1	18
α-helix	495-496	2
β-strand	502	1	17
β-strand	504-507	4	19
β-strand	515-518	4	19
β-strand	536-538	3	16
β-strand	550	1	20
α-helix	553-555	3
β-strand	556	1	21
β-strand	558	1	17
β-strand	564	1	18
β-strand	567	1	21
α-helix	569-571	3
β-strand	573	1	20
β-strand	575-579	5	15
β-strand	581	1	14
β-strand	585-597	13	14
β-strand	602-604	3	14
β-strand	619-624	6	12
β-strand	627-636	10	12
β-strand	647-649	3	12
β-strand	655-659	5	12
β-strand	666-670	5	12
α-helix	671-673	3
β-strand	677-681	5	11
β-strand	689-693	5	11
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	11
β-strand	718-721	4	11
β-strand	724-731	8	22
β-strand	737	1	22
β-strand	742-746	5	22
β-strand	762-767	6	22
β-strand	773-775	3	23
β-strand	786-804	19	24
β-strand	809-812	4	25
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	836-861	26
β-strand	866-868	3	26
β-strand	878-879	2	27
β-strand	882-883	2	27
α-helix	902-909	8
α-helix	917-922	6
α-helix	923-925	3
α-helix	934-940	7
β-strand	943-946	4	25
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	1025-1044	20
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	24
β-strand	1140-1159	20	24
β-strand	1162-1164	3	28
β-strand	1168-1172	5	28
β-strand	1175-1180	6	24
β-strand	1183-1188	6	24
β-strand	1195	1	24
β-strand	1202-1205	4	28
β-strand	1213-1214	2	28

Chain C: 37 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	49	1	29
β-strand	54-56	3	12
β-strand	59-67	9	30
α-helix	68-69	2
β-strand	75-76	2	31
β-strand	80	1	32
α-helix	87-90	4
β-strand	97	1	33
β-strand	101-107	7	31
β-strand	109-112	4	34
β-strand	117-120	4	34
β-strand	124-127	4	33
β-strand	136-141	6	33
β-strand	145-151	7	33
β-strand	155	1	35
β-strand	161	1	32
β-strand	175	1	35
β-strand	185-190	6	33
β-strand	197-205	9	31
β-strand	208-214	7	31
β-strand	220	1	29
β-strand	221-227	7	31
β-strand	234-236	3	33
β-strand	240	1	32
β-strand	256-260	5	31
β-strand	262-270	9	30
β-strand	276-281	6	30
α-helix	287-294	8
α-helix	299-300	2
β-strand	302-306	5	36
β-strand	315-319	5	37
α-helix	324-325	2
β-strand	326	1	38
α-helix	329-333	5
β-strand	337-339	3	39
α-helix	341-343	3
β-strand	345-349	5	40
β-strand	353	1	38
β-strand	354	1	41
α-helix	356-361	6
β-strand	364-371	8	40
α-helix	375-377	3
β-strand	382-383	2	42
β-strand	385-392	8	40
α-helix	398-401	4
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	40
β-strand	435-437	3	39
β-strand	459-462	4	43
β-strand	466-468	3	44
β-strand	477	1	45
α-helix	479-481	3
α-helix	489-491	3
β-strand	492	1	45
β-strand	494	1	46
α-helix	495-496	2
β-strand	502	1	45
β-strand	505-507	3	47
β-strand	515-517	3	47
β-strand	522	1	48
β-strand	527	1	48
β-strand	536-538	3	44
α-helix	540-541	2
β-strand	549	1	44
β-strand	551	1	49
α-helix	553-555	3
β-strand	556	1	50
β-strand	564	1	46
β-strand	567	1	50
α-helix	569-571	3
β-strand	572	1	49
β-strand	576-579	4	43
β-strand	581	1	40
β-strand	585-595	11	40
β-strand	602-603	2	42
β-strand	604	1	41
β-strand	616	1	37
β-strand	619-624	6	37
β-strand	627-636	10	37
β-strand	647-649	3	37
β-strand	655-659	5	37
β-strand	666-670	5	37
α-helix	671-673	3
β-strand	677-681	5	36
β-strand	689-693	5	36
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	36
β-strand	718-721	4	36
β-strand	724-731	8	51
β-strand	737-739	3	51
β-strand	742-746	5	51
β-strand	762-767	6	51
β-strand	773-775	3	52
β-strand	782	1	53
β-strand	785	1	53
β-strand	786-804	19	54
β-strand	809-812	4	55
α-helix	814-818	5
α-helix	823-829	7
α-helix	835-862	28
β-strand	866-868	3	23
β-strand	878-879	2	56
β-strand	882-883	2	56
α-helix	902-910	9
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	55
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	1001-1016	16
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1070-1109	40
α-helix	1110-1114	5
β-strand	1129-1137	9	54
β-strand	1140-1159	20	54
β-strand	1162-1164	3	57
β-strand	1168-1172	5	57
β-strand	1175-1179	5	54
β-strand	1184-1188	5	54
β-strand	1195	1	54
β-strand	1202-1205	4	57
β-strand	1213-1215	3	57

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

>8Y1C_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
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
8Y1H 3.16 Å, The 2up formation of the HKU1-B S protein in the apo state

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