8Y1G: Spike glycoprotein

The 1up conformation of the HKU1-B S protein in the apo state. Determined by electron microscopy at 2.99 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.99 Å
Organism: Human coronavirus HKU1 (isolate N2)
Chains: 3
Atoms: 29,541
Mol. weight: 450.02 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1G contains 108 α-helices and 299 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: 35 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25	1	2
α-helix	32-34	3
β-strand	39	1	3
α-helix	42-44	3
β-strand	49	1	4
β-strand	54-55	2	5
β-strand	59-61	3	6
β-strand	64-67	4	7
α-helix	68-69	2
β-strand	73	1	3
β-strand	76	1	8
β-strand	80-81	2	9
β-strand	85	1	2
α-helix	87-90	4
β-strand	97	1	10
β-strand	101-107	7	8
β-strand	109-113	5	11
β-strand	116-120	5	11
β-strand	124-127	4	10
β-strand	136-138	3	10
β-strand	141	1	10
β-strand	145-151	7	10
β-strand	155	1	12
β-strand	156	1	1
β-strand	161-162	2	9
β-strand	175	1	12
β-strand	183-190	8	10
β-strand	197-203	7	8
β-strand	210-214	5	8
β-strand	220	1	4
β-strand	221-225	5	8
β-strand	234-237	4	10
β-strand	240-241	2	9
β-strand	256-260	5	8
β-strand	262-265	4	7
β-strand	266	1	13
β-strand	268-270	3	6
β-strand	276-278	3	6
β-strand	281	1	13
α-helix	287-294	8
α-helix	299-300	2
β-strand	302-307	6	14
β-strand	316	1	15
α-helix	325	1
β-strand	326	1	16
α-helix	327	1
α-helix	329-333	5
β-strand	337-339	3	17
β-strand	345-348	4	18
β-strand	353	1	16
α-helix	356-362	7
β-strand	364-368	5	18
α-helix	377-380	4
β-strand	383	1	19
β-strand	387-392	6	18
α-helix	393-394	2
α-helix	395-401	7
α-helix	409-413	5
β-strand	415	1	20
β-strand	422-428	7	18
β-strand	430	1	21
β-strand	435-437	3	17
β-strand	459	1	22
β-strand	462-463	2	23
β-strand	466-468	3	24
β-strand	473	1	25
α-helix	481-484	4
α-helix	489-491	3
β-strand	492	1	26
β-strand	494	1	27
β-strand	500	1	25
α-helix	501-503	3
β-strand	504-507	4	28
β-strand	515-518	4	28
β-strand	536-538	3	24
β-strand	542	1	20
β-strand	550-551	2	29
β-strand	558	1	26
β-strand	564	1	27
β-strand	572-573	2	29
β-strand	575-576	2	23
β-strand	579	1	22
β-strand	581	1	30
β-strand	585	1	21
β-strand	586	1	30
β-strand	588-593	6	18
β-strand	602	1	19
β-strand	603	1	16
β-strand	619-624	6	15
β-strand	627-633	7	15
β-strand	636	1	31
β-strand	647-649	3	31
β-strand	655-660	6	31
β-strand	665-667	3	31
β-strand	669-670	2	15
β-strand	676-681	6	14
β-strand	689-693	5	14
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	14
β-strand	718-721	4	14
β-strand	724-731	8	32
β-strand	742-746	5	32
β-strand	762-767	6	32
β-strand	773-775	3	33
β-strand	786-789	4	34
β-strand	794-795	2	35
β-strand	798-804	7	36
β-strand	809-812	4	37
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	38
β-strand	878	1	39
β-strand	883	1	39
α-helix	902-908	7
α-helix	915-922	8
α-helix	934-939	6
β-strand	943-946	4	37
α-helix	947-948	2
α-helix	952-965	14
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1016	16
α-helix	1024-1044	21
α-helix	1058-1061	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	36
β-strand	1140-1147	8	36
β-strand	1149-1150	2	35
β-strand	1155-1159	5	34
β-strand	1162-1163	2	40
β-strand	1169-1172	4	40
β-strand	1176-1180	5	34
β-strand	1183-1187	5	34
β-strand	1195	1	34
β-strand	1202-1205	4	40
β-strand	1213-1214	2	40

Chain B: 35 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	41
β-strand	46	1	42
β-strand	48	1	42
β-strand	49	1	43
β-strand	54-55	2	31
β-strand	59-61	3	44
β-strand	64-67	4	45
α-helix	68-69	2
β-strand	75-76	2	46
β-strand	80-81	2	47
α-helix	87-89	3
β-strand	96-97	2	48
β-strand	101-107	7	46
β-strand	110-111	2	49
β-strand	118-119	2	49
β-strand	123-126	4	50
β-strand	136-141	6	50
β-strand	145-151	7	50
β-strand	155	1	51
β-strand	156	1	41
β-strand	161-162	2	47
β-strand	167	1	52
β-strand	175	1	51
β-strand	185-190	6	50
β-strand	197-205	9	46
β-strand	208-214	7	46
β-strand	220	1	43
β-strand	221-224	4	46
β-strand	227	1	46
β-strand	234-235	2	48
β-strand	236-238	3	50
α-helix	239	1
β-strand	240-241	2	47
β-strand	242	1	52
β-strand	256-260	5	46
β-strand	262-265	4	45
β-strand	266-270	5	44
β-strand	276-281	6	44
α-helix	286-293	8
β-strand	302-306	5	53
β-strand	316-319	4	54
β-strand	326	1	55
α-helix	330-333	4
β-strand	337-339	3	56
β-strand	345-350	6	57
β-strand	353	1	55
β-strand	354	1	58
α-helix	356-361	6
β-strand	365-368	4	57
β-strand	371	1	57
α-helix	378-380	3
β-strand	383-392	10	57
α-helix	395-400	6
α-helix	409-412	4
β-strand	422-430	9	57
β-strand	435-437	3	56
α-helix	443-447	5
β-strand	459-463	5	59
β-strand	467-468	2	60
α-helix	476	1
β-strand	477	1	61
α-helix	478	1
α-helix	489-491	3
β-strand	492	1	61
β-strand	494	1	62
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-507	4	63
β-strand	515-518	4	63
β-strand	536-537	2	60
α-helix	553-555	3
β-strand	558	1	61
β-strand	564	1	62
β-strand	575-579	5	59
β-strand	581	1	57
β-strand	585-597	13	57
β-strand	604	1	58
β-strand	616	1	54
β-strand	619-624	6	54
β-strand	627-636	10	54
β-strand	647-649	3	64
β-strand	655-658	4	64
β-strand	659	1	54
β-strand	666-670	5	54
β-strand	677-681	5	53
β-strand	689-693	5	53
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	53
β-strand	718-721	4	53
β-strand	724-731	8	65
β-strand	737	1	65
β-strand	742-746	5	65
β-strand	762-767	6	65
β-strand	773-775	3	66
β-strand	786-795	10	67
β-strand	798-804	7	68
β-strand	809-812	4	69
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-861	26
β-strand	866-868	3	33
β-strand	878-879	2	70
β-strand	882-883	2	70
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	69
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	1045-1047	3
α-helix	1058-1061	4
α-helix	1070-1109	40
α-helix	1110-1114	5
β-strand	1129-1137	9	68
β-strand	1140-1147	8	68
β-strand	1149-1158	10	67
β-strand	1159	1	71
β-strand	1162-1163	2	72
β-strand	1169-1172	4	72
β-strand	1175-1179	5	71
β-strand	1184-1188	5	71
β-strand	1195	1	71
β-strand	1202-1205	4	72
β-strand	1213-1214	2	72

Chain C: 38 helices, 98 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	73
β-strand	25	1	74
α-helix	32-34	3
β-strand	38-39	2	75
β-strand	49	1	76
β-strand	54-56	3	64
β-strand	59-67	9	77
α-helix	68-69	2
β-strand	73-74	2	75
β-strand	75-76	2	78
β-strand	80-81	2	79
β-strand	85	1	74
α-helix	87-90	4
β-strand	96-97	2	80
β-strand	101-107	7	78
β-strand	109-112	4	81
β-strand	117-120	4	81
β-strand	124-127	4	80
β-strand	136-141	6	80
β-strand	145-151	7	80
β-strand	155	1	82
β-strand	156	1	73
β-strand	161-162	2	79
β-strand	175	1	82
β-strand	183-190	8	80
β-strand	197-205	9	78
β-strand	208-214	7	78
β-strand	220	1	76
β-strand	221-227	7	78
β-strand	234-237	4	80
β-strand	240-241	2	79
β-strand	256-260	5	78
β-strand	262-270	9	77
β-strand	276-281	6	77
α-helix	287-294	8
α-helix	299-300	2
β-strand	302-310	9	83
α-helix	311-313	3
β-strand	315-319	5	5
β-strand	326	1	84
α-helix	329-333	5
β-strand	337-339	3	85
β-strand	345-349	5	86
β-strand	353-354	2	84
α-helix	356-361	6
β-strand	364-368	5	86
β-strand	371	1	86
β-strand	385-392	8	86
α-helix	393-394	2
α-helix	398-401	4
α-helix	409-412	4
β-strand	422-423	2	86
β-strand	425-430	6	86
β-strand	435-437	3	85
α-helix	443-446	4
β-strand	459-463	5	87
β-strand	466-468	3	88
β-strand	477	1	89
α-helix	478	1
α-helix	479-481	3
β-strand	492	1	89
β-strand	494	1	90
α-helix	501-503	3
β-strand	504-507	4	91
β-strand	515-518	4	91
β-strand	536-538	3	88
α-helix	540-541	2
α-helix	549	1
β-strand	550-551	2	92
β-strand	558	1	89
β-strand	564	1	90
α-helix	569-571	3
β-strand	572-573	2	92
β-strand	575-579	5	87
β-strand	581	1	86
β-strand	585-595	11	86
β-strand	603-604	2	84
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	674-681	8	83
β-strand	689-693	5	83
α-helix	697-703	7
β-strand	712-714	3	83
β-strand	718-721	4	83
β-strand	724-731	8	93
β-strand	737-739	3	93
β-strand	742-746	5	93
β-strand	762-767	6	93
β-strand	773-775	3	38
β-strand	782	1	94
β-strand	785	1	94
β-strand	786-791	6	95
β-strand	794-804	11	96
β-strand	809-812	4	97
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-862	27
β-strand	866-868	3	66
β-strand	878-879	2	98
β-strand	882-883	2	98
α-helix	885-887	3
α-helix	902-909	8
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	97
α-helix	947-948	2
α-helix	953-964	12
α-helix	979-988	10
α-helix	996-999	4
α-helix	1001-1016	16
α-helix	1024-1044	21
α-helix	1045-1047	3
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1125	1	99
β-strand	1127	1	99
β-strand	1129	1	96
β-strand	1134-1137	4	96
β-strand	1140-1150	11	96
β-strand	1153-1158	6	95
β-strand	1162-1163	2	100
α-helix	1165-1167	3
β-strand	1169-1172	4	100
β-strand	1175-1176	2	101
β-strand	1179	1	102
β-strand	1184	1	102
β-strand	1186	1	103
β-strand	1187-1188	2	101
β-strand	1195	1	103
β-strand	1202-1205	4	100
β-strand	1213-1214	2	100

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

>8Y1G_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
8Y1H 3.16 Å, The 2up formation of the HKU1-B S protein in the apo state

Browse structure collections

About this viewer

MolViewer shows 8Y1G 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.