8Y19: Spike glycoprotein

Closed conformation of HKU1-B S protein after incubation of the receptor. Determined by electron microscopy at 2.3 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Human coronavirus HKU1 (isolate N2)
Chains: 3
Atoms: 29,541
Mol. weight: 450.02 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y19 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y19 contains 129 α-helices and 279 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: 43 helices, 93 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	54-56	3	5
β-strand	59-68	10	6
α-helix	69	1
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	261-270	10	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
α-helix	324-325	2
β-strand	326	1	15
α-helix	329-333	5
β-strand	337-339	3	16
β-strand	345-349	5	15
β-strand	353-354	2	15
α-helix	356-362	7
β-strand	364-371	8	15
α-helix	375-377	3
β-strand	382-392	11	15
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	15
β-strand	435-437	3	16
α-helix	443-447	5
β-strand	459-463	5	17
β-strand	466-468	3	18
β-strand	477	1	19
α-helix	478	1
α-helix	482-484	3
β-strand	492	1	19
β-strand	494	1	20
α-helix	495-496	2
α-helix	500-501	2
β-strand	502	1	19
α-helix	503	1
β-strand	504-507	4	21
β-strand	515-518	4	21
β-strand	536-538	3	18
β-strand	550-551	2	22
α-helix	553-555	3
β-strand	556	1	23
β-strand	558	1	19
β-strand	564	1	20
β-strand	567	1	23
α-helix	569-571	3
β-strand	572-573	2	22
β-strand	575-579	5	17
β-strand	581-582	2	15
β-strand	585-597	13	15
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	712-715	4	12
β-strand	718-721	4	12
β-strand	724-731	8	24
β-strand	737-739	3	24
β-strand	742-746	5	24
β-strand	762-767	6	24
β-strand	773-775	3	25
β-strand	782	1	26
β-strand	785	1	26
β-strand	786-804	19	27
β-strand	809-812	4	28
α-helix	814-818	5
α-helix	823-830	8
α-helix	835-862	28
β-strand	866-868	3	29
β-strand	878-879	2	30
β-strand	882-883	2	30
α-helix	902-908	7
α-helix	915-922	8
α-helix	934-940	7
β-strand	943-946	4	28
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	1058-1062	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	27
β-strand	1140-1158	19	27
β-strand	1159	1	31
β-strand	1162-1164	3	32
β-strand	1168-1172	5	32
β-strand	1175-1180	6	31
β-strand	1183-1188	6	31
β-strand	1191-1195	5	31
β-strand	1202-1205	4	32
β-strand	1213-1214	2	32

Chains B and C: 43 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	33
β-strand	25-26	2	34
α-helix	32-34	3
β-strand	38-39	2	35
β-strand	49	1	36
β-strand	54-55	2	14
β-strand	59-68	10	37
α-helix	69	1
β-strand	73-74	2	35
β-strand	75-76	2	38
β-strand	80-81	2	39
β-strand	85-86	2	34
α-helix	87-90	4
β-strand	96-97	2	40
β-strand	101-107	7	38
β-strand	109-112	4	41
β-strand	117-120	4	41
β-strand	124-127	4	40
β-strand	136-141	6	40
β-strand	145-151	7	40
β-strand	155-160	6	42
β-strand	161-162	2	39
α-helix	171-172	2
β-strand	173-175	3	42
β-strand	183-190	8	40
β-strand	197-205	9	38
β-strand	208-214	7	38
β-strand	220	1	36
β-strand	221-227	7	38
β-strand	234-237	4	40
α-helix	238-239	2
β-strand	240-241	2	39
β-strand	256-260	5	38
β-strand	261-270	10	37
β-strand	276-281	6	37
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	43
β-strand	309-310	2	44
α-helix	311-313	3
β-strand	315-319	5	45
α-helix	324-325	2
β-strand	326	1	46
α-helix	329-333	5
β-strand	337-339	3	47
β-strand	345-349	5	46
β-strand	353-354	2	46
α-helix	356-362	7
β-strand	364-371	8	46
α-helix	375-377	3
β-strand	382-392	11	46
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	46
β-strand	435-437	3	47
α-helix	443-447	5
β-strand	459-463	5	48
β-strand	466-468	3	49
β-strand	477	1	50
α-helix	478	1
α-helix	482-484	3
β-strand	492	1	50
β-strand	494	1	51
α-helix	495-496	2
α-helix	500-501	2
β-strand	502	1	50
α-helix	503	1
β-strand	504-507	4	52
β-strand	515-518	4	52
β-strand	536-538	3	49
β-strand	550-551	2	53
α-helix	553-555	3
β-strand	556	1	54
β-strand	558	1	50
β-strand	564	1	51
β-strand	567	1	54
α-helix	569-571	3
β-strand	572-573	2	53
β-strand	575-579	5	48
β-strand	581-582	2	46
β-strand	585-597	13	46
β-strand	602-604	3	46
β-strand	619-624	6	45
β-strand	627-636	10	45
β-strand	647-649	3	45
β-strand	655-659	5	45
β-strand	666-670	5	45
α-helix	671-673	3
β-strand	674-675	2	44
β-strand	678-681	4	43
β-strand	689-693	5	43
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	43
β-strand	718-721	4	43
β-strand	724-731	8	55
β-strand	737-739	3	55
β-strand	742-746	5	55
β-strand	762-767	6	55
β-strand	773-775	3	56
β-strand	782	1	57
β-strand	785	1	57
β-strand	786-804	19	58
β-strand	809-812	4	59
α-helix	814-818	5
α-helix	823-830	8
α-helix	835-862	28
β-strand	866-868	3	25
β-strand	878-879	2	60
β-strand	882-883	2	60
α-helix	902-908	7
α-helix	915-922	8
α-helix	934-940	7
β-strand	943-946	4	59
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	1058-1062	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	58
β-strand	1140-1158	19	58
β-strand	1159	1	61
β-strand	1162-1164	3	62
β-strand	1168-1172	5	62
β-strand	1175-1180	6	61
β-strand	1183-1188	6	61
β-strand	1191-1195	5	61
β-strand	1202-1205	4	62
β-strand	1213-1214	2	62

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

>8Y19_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:

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

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