8Y1D: Spike glycoprotein

2up-TM conformation of HKU1-B S protein after incubation of the receptor. Determined by electron microscopy at 2.7 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Human coronavirus HKU1 (isolate N2), Homo sapiens
Chains: 5
Atoms: 34,921
Mol. weight: 534.76 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1D contains 131 α-helices and 342 β-strands across 5 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: 42 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	32-34	3
β-strand	38-39	2	2
β-strand	49	1	3
β-strand	54-55	2	4
β-strand	59-67	9	5
α-helix	68-69	2
β-strand	73-74	2	2
β-strand	75-76	2	6
β-strand	80-81	2	7
β-strand	85-86	2	1
α-helix	87-90	4
β-strand	96-97	2	8
β-strand	101-107	7	6
β-strand	109-112	4	9
β-strand	117-120	4	9
β-strand	124-127	4	8
β-strand	136-141	6	8
β-strand	145-151	7	8
β-strand	155	1	10
β-strand	161-162	2	7
α-helix	171-172	2
β-strand	175	1	10
β-strand	183-190	8	8
β-strand	197-205	9	6
β-strand	208-214	7	6
β-strand	220	1	3
β-strand	221-227	7	6
β-strand	234-237	4	8
β-strand	240-241	2	7
β-strand	256-260	5	6
β-strand	262-270	9	5
β-strand	276-281	6	5
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-307	6	11
β-strand	319	1	12
α-helix	325-326	2
α-helix	330-333	4
α-helix	338	1
β-strand	339	1	13
α-helix	340	1
β-strand	347-349	3	14
β-strand	353	1	15
α-helix	357-362	6
β-strand	365-368	4	16
α-helix	377-380	4
β-strand	382-383	2	15
β-strand	385-388	4	14
β-strand	389-392	4	16
α-helix	395-401	7
α-helix	409-412	4
β-strand	422	1	17
β-strand	425-427	3	16
β-strand	430	1	18
β-strand	437	1	13
α-helix	443-446	4
β-strand	459-463	5	19
β-strand	467-468	2	20
β-strand	477	1	21
α-helix	479-482	4
β-strand	487	1	22
α-helix	489-491	3
β-strand	492	1	21
β-strand	494	1	23
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-505	2	24
β-strand	515	1	22
β-strand	517-518	2	24
α-helix	524-526	3
β-strand	536-537	2	20
α-helix	549	1
β-strand	550-551	2	25
α-helix	552	1
β-strand	558	1	21
β-strand	564	1	23
β-strand	572-573	2	25
β-strand	575-579	5	19
β-strand	581-582	2	18
β-strand	585-586	2	18
β-strand	588-591	4	16
β-strand	593	1	17
β-strand	594-595	2	14
β-strand	602-603	2	15
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	676-681	6	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	26
β-strand	736-737	2	26
β-strand	742-746	5	26
β-strand	762-767	6	26
β-strand	773-775	3	27
β-strand	786-804	19	28
β-strand	809-812	4	29
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	30
β-strand	878-879	2	31
β-strand	882-883	2	31
α-helix	902-908	7
α-helix	917-922	6
α-helix	934-939	6
β-strand	943-946	4	29
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	28
β-strand	1140-1158	19	28
β-strand	1159	1	32
β-strand	1162-1164	3	33
β-strand	1168-1172	5	33
β-strand	1175-1180	6	32
β-strand	1183-1188	6	32
β-strand	1195	1	32
β-strand	1202-1205	4	33
β-strand	1213-1214	2	33

Chain B: 36 helices, 94 β-strands

Element	Residues	Length	Sheet
α-helix	42-44	3
β-strand	46	1	34
β-strand	48	1	34
β-strand	49	1	35
β-strand	54-55	2	12
β-strand	59-64	6	36
β-strand	67	1	37
β-strand	80-81	2	38
α-helix	88-90	3
β-strand	96-97	2	39
β-strand	101-107	7	40
β-strand	109-112	4	41
β-strand	117-120	4	41
β-strand	124-127	4	39
β-strand	136-141	6	39
β-strand	145-151	7	39
β-strand	155	1	42
β-strand	161	1	38
β-strand	175	1	42
β-strand	183-190	8	39
β-strand	197-205	9	40
β-strand	208-214	7	40
β-strand	220	1	35
β-strand	221-227	7	40
β-strand	234-237	4	39
β-strand	240-241	2	38
β-strand	256-260	5	40
β-strand	262	1	37
β-strand	265-270	6	36
β-strand	276-281	6	36
α-helix	286-294	9
β-strand	302-307	6	43
β-strand	318-319	2	44
β-strand	326	1	45
α-helix	330-333	4
α-helix	338	1
β-strand	339	1	46
α-helix	340	1
β-strand	347-349	3	47
β-strand	353-354	2	45
α-helix	357-362	6
β-strand	365-368	4	48
α-helix	377-380	4
β-strand	382-383	2	45
β-strand	385-388	4	47
β-strand	389-392	4	48
α-helix	395-401	7
α-helix	409-412	4
β-strand	422	1	49
β-strand	425-427	3	48
β-strand	430	1	50
β-strand	437	1	46
α-helix	443-446	4
β-strand	459-463	5	51
β-strand	467-468	2	52
β-strand	477	1	53
α-helix	479-482	4
β-strand	487	1	54
α-helix	489-491	3
β-strand	492	1	53
β-strand	494	1	55
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-505	2	56
β-strand	515	1	54
β-strand	517-518	2	56
α-helix	524-526	3
β-strand	536-537	2	52
α-helix	549	1
β-strand	550-551	2	57
α-helix	552	1
β-strand	558	1	53
β-strand	564	1	55
β-strand	572-573	2	57
β-strand	575-579	5	51
β-strand	581-582	2	50
β-strand	585-586	2	50
β-strand	588-591	4	48
β-strand	593	1	49
β-strand	594-595	2	47
β-strand	602-604	3	45
β-strand	619-624	6	44
β-strand	627-635	9	44
β-strand	647-649	3	44
β-strand	655-660	6	44
β-strand	665-670	6	44
α-helix	671-673	3
β-strand	676-681	6	43
β-strand	689-693	5	43
α-helix	697-703	7
β-strand	712-715	4	43
β-strand	718-721	4	43
β-strand	724-731	8	58
β-strand	737-739	3	58
β-strand	742-746	5	58
β-strand	762-767	6	58
β-strand	773-775	3	59
β-strand	782	1	60
β-strand	785	1	60
β-strand	786-804	19	61
β-strand	809-812	4	62
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-862	27
β-strand	866-868	3	27
β-strand	878-879	2	63
β-strand	882-883	2	63
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	62
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1017	17
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	61
β-strand	1140-1159	20	61
β-strand	1162-1164	3	64
β-strand	1168-1172	5	64
β-strand	1175-1180	6	61
β-strand	1183-1188	6	61
β-strand	1195	1	61
β-strand	1202-1205	4	64
β-strand	1213-1214	2	64

Chain C: 33 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	65
β-strand	46	1	66
β-strand	48	1	66
β-strand	49	1	67
β-strand	54-55	2	44
β-strand	59-67	9	68
β-strand	75-76	2	69
β-strand	80-81	2	70
α-helix	87-89	3
β-strand	96-97	2	71
β-strand	101-107	7	69
β-strand	109-112	4	72
β-strand	117-120	4	72
β-strand	124-127	4	71
β-strand	136-141	6	71
β-strand	145-151	7	71
β-strand	155	1	73
β-strand	156	1	65
β-strand	161	1	70
β-strand	175	1	73
β-strand	185-190	6	71
β-strand	197-205	9	69
β-strand	208-214	7	69
β-strand	220	1	67
β-strand	221-227	7	69
β-strand	234-237	4	71
β-strand	240-241	2	70
β-strand	256-260	5	69
β-strand	262-270	9	68
β-strand	276-281	6	68
α-helix	287-294	8
β-strand	302-306	5	74
β-strand	316-319	4	4
β-strand	326	1	75
α-helix	329-333	5
β-strand	337-339	3	76
β-strand	345-349	5	75
β-strand	353-354	2	75
α-helix	356-362	7
β-strand	364-371	8	75
α-helix	375-377	3
β-strand	382-392	11	75
α-helix	393-394	2
α-helix	396-401	6
α-helix	409-412	4
α-helix	415-417	3
β-strand	422-430	9	75
β-strand	435-437	3	76
β-strand	459-463	5	77
β-strand	466-468	3	78
β-strand	473-477	5	79
α-helix	481-483	3
β-strand	487	1	80
β-strand	492	1	79
β-strand	494	1	81
β-strand	500-502	3	79
β-strand	504-507	4	80
β-strand	515-518	4	80
β-strand	536-538	3	78
α-helix	540-541	2
β-strand	550-551	2	82
α-helix	553-555	3
β-strand	558	1	79
β-strand	564	1	81
β-strand	572-573	2	82
β-strand	575-579	5	77
β-strand	581-582	2	75
β-strand	585-597	13	75
β-strand	602-604	3	75
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	74
β-strand	689-693	5	74
α-helix	697-703	7
β-strand	712-715	4	74
β-strand	718-721	4	74
β-strand	724-731	8	83
β-strand	737	1	83
β-strand	742-746	5	83
β-strand	762-767	6	83
β-strand	773-775	3	30
β-strand	782	1	84
β-strand	785	1	84
β-strand	786-804	19	85
β-strand	809-812	4	86
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	59
β-strand	878-879	2	87
β-strand	882-883	2	87
α-helix	885-887	3
α-helix	902-909	8
α-helix	915-922	8
α-helix	923-925	3
α-helix	934-940	7
β-strand	943-946	4	86
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	1059-1062	4
α-helix	1070-1109	40
α-helix	1110-1114	5
β-strand	1125	1	88
β-strand	1127	1	88
β-strand	1129-1137	9	85
β-strand	1140-1159	20	85
β-strand	1162-1164	3	89
β-strand	1168-1172	5	89
β-strand	1175-1180	6	85
β-strand	1183-1188	6	85
β-strand	1195	1	85
β-strand	1202-1205	4	89
β-strand	1213-1214	2	89

Chains D and E: 10 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	149-150	2	90
α-helix	157-158	2
β-strand	159-162	4	90
β-strand	167-170	4	90
β-strand	171	1	91
β-strand	172	1	92
α-helix	178-181	4
β-strand	196-200	5	92
β-strand	209-212	4	91
β-strand	225-228	4	91
β-strand	236-240	5	92
α-helix	261-263	3
β-strand	270	1	93
β-strand	273-274	2	94
β-strand	279-281	3	94
β-strand	284-285	2	93
β-strand	290-294	5	93
α-helix	295-297	3
α-helix	305-307	3
β-strand	309-310	2	94
β-strand	328	1	95
β-strand	346-350	5	93
β-strand	351	1	95
α-helix	363-366	4
β-strand	378-381	4	96
β-strand	383	1	97
β-strand	386	1	98
β-strand	398	1	97
β-strand	401-403	3	96
α-helix	407-410	4
β-strand	425-427	3	99
β-strand	428	1	96
β-strand	439	1	98
β-strand	445-447	3	96
α-helix	449-451	3
β-strand	454-458	5	96
β-strand	467	1	100
β-strand	470	1	100
β-strand	472-474	3	99
β-strand	475-476	2	96
α-helix	484-486	3
α-helix	489-491	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1290	Human coronavirus HKU1 (isolate N2)	Q14EB0
Transmembrane protease serine 2	D, E	protein	384	Homo sapiens	O15393 (AlphaFold model)

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

>8Y1D_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

Sequence of entity 2 (D, E), FASTA

>8Y1D_2 Transmembrane protease serine 2 (chains D, E)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNSSRQSQIVGGESALPGAWPWQVSLHVQNVHVCGGSIITP
EWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIAL
MKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQ
RCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKA
YRPGVYGNVMVFTDWIYRQMRADG

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
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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