8Y1E: Spike glycoprotein

3up-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: 6
Atoms: 37,611
Mol. weight: 577.13 kDa
Ligands: NAG
Released: 1 May 2024

Explore 8Y1E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y1E contains 147 α-helices and 381 β-strands across 6 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: 39 helices, 100 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	35	1	2
β-strand	46	1	3
β-strand	48	1	3
β-strand	49	1	4
β-strand	54-56	3	5
β-strand	59-63	5	6
β-strand	66-67	2	7
β-strand	75	1	2
β-strand	76	1	8
β-strand	80-81	2	9
α-helix	88-90	3
β-strand	96-97	2	10
β-strand	101-107	7	8
β-strand	109-112	4	11
β-strand	117-120	4	11
β-strand	124-127	4	10
β-strand	136-141	6	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	185-190	6	10
β-strand	197-205	9	8
β-strand	208-214	7	8
β-strand	220	1	4
β-strand	221-226	6	8
β-strand	234-237	4	10
β-strand	240-241	2	9
β-strand	256-260	5	8
β-strand	262-263	2	7
β-strand	266-270	5	6
β-strand	276-281	6	6
α-helix	287-294	8
α-helix	299-300	2
β-strand	302-308	7	13
β-strand	316-319	4	14
β-strand	326	1	15
α-helix	330-333	4
α-helix	338	1
β-strand	339	1	16
α-helix	340	1
β-strand	347-349	3	17
β-strand	353	1	15
α-helix	357-362	6
β-strand	365-368	4	18
α-helix	377-380	4
β-strand	382-383	2	15
β-strand	385-388	4	17
β-strand	389-392	4	18
α-helix	395-401	7
α-helix	409-412	4
β-strand	422	1	19
β-strand	425-427	3	18
β-strand	430	1	20
β-strand	437	1	16
α-helix	443-446	4
β-strand	459-463	5	21
β-strand	467-468	2	22
β-strand	477	1	23
α-helix	479-482	4
β-strand	487	1	24
α-helix	489-491	3
β-strand	492	1	23
β-strand	494	1	25
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-505	2	26
β-strand	515	1	24
β-strand	517-518	2	26
α-helix	524-526	3
β-strand	536-537	2	22
α-helix	549	1
β-strand	550-551	2	27
α-helix	552	1
β-strand	558	1	23
β-strand	564	1	25
β-strand	572-573	2	27
β-strand	575-579	5	21
β-strand	581-582	2	20
β-strand	585-586	2	20
β-strand	588-591	4	18
β-strand	593	1	19
β-strand	594-595	2	17
β-strand	602-603	2	15
β-strand	619-624	6	14
β-strand	627-636	10	14
β-strand	647-649	3	14
β-strand	655-660	6	14
β-strand	665-670	6	14
α-helix	671-673	3
β-strand	675-681	7	13
β-strand	689-693	5	13
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	13
β-strand	718-721	4	13
β-strand	724-731	8	28
β-strand	737	1	28
β-strand	742-746	5	28
β-strand	762-767	6	28
β-strand	773-775	3	29
β-strand	782	1	30
β-strand	785	1	30
β-strand	786-804	19	31
β-strand	809-812	4	32
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	836-860	25
β-strand	866-868	3	33
β-strand	878-879	2	34
β-strand	882-883	2	34
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	32
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	31
β-strand	1140-1158	19	31
β-strand	1159	1	35
β-strand	1162-1164	3	36
β-strand	1168-1172	5	36
β-strand	1175-1180	6	35
β-strand	1183-1188	6	35
β-strand	1195	1	35
β-strand	1202-1205	4	36
α-helix	1212	1
β-strand	1213-1215	3	36

Chain B: 36 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	37
β-strand	48	1	37
β-strand	49	1	38
β-strand	54-55	2	14
β-strand	59-67	9	39
β-strand	75-76	2	40
α-helix	88-90	3
β-strand	96-97	2	41
β-strand	101-107	7	40
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	44
β-strand	173-175	3	43
β-strand	183-190	8	41
β-strand	197-205	9	40
β-strand	208-214	7	40
β-strand	220	1	38
β-strand	221-227	7	40
β-strand	234-237	4	41
α-helix	238-239	2
β-strand	240-241	2	44
β-strand	256-260	5	40
β-strand	262-270	9	39
β-strand	276-281	6	39
α-helix	286-294	9
β-strand	302-307	6	45
β-strand	318-319	2	46
β-strand	326	1	47
α-helix	330-333	4
α-helix	338	1
β-strand	339	1	48
α-helix	340	1
β-strand	347-349	3	49
β-strand	353-354	2	47
α-helix	357-362	6
β-strand	365-368	4	50
α-helix	377-380	4
β-strand	382-383	2	47
β-strand	385-388	4	49
β-strand	389-392	4	50
α-helix	395-401	7
α-helix	409-412	4
β-strand	422	1	51
β-strand	425-427	3	50
β-strand	430	1	52
β-strand	437	1	48
α-helix	443-446	4
β-strand	459-463	5	53
β-strand	467-468	2	54
β-strand	477	1	55
α-helix	479-482	4
β-strand	487	1	56
α-helix	489-491	3
β-strand	492	1	55
β-strand	494	1	57
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-505	2	58
β-strand	515	1	56
β-strand	517-518	2	58
α-helix	524-526	3
β-strand	536-537	2	54
α-helix	549	1
β-strand	550-551	2	59
α-helix	552	1
β-strand	558	1	55
β-strand	564	1	57
β-strand	572-573	2	59
β-strand	575-579	5	53
β-strand	581-582	2	52
β-strand	585-586	2	52
β-strand	588-591	4	50
β-strand	593	1	51
β-strand	594-595	2	49
β-strand	602-604	3	47
β-strand	619-624	6	46
β-strand	627-636	10	46
β-strand	647-649	3	46
β-strand	655-660	6	46
β-strand	665-670	6	46
α-helix	671-673	3
β-strand	676-681	6	45
β-strand	689-693	5	45
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-715	4	45
β-strand	718-721	4	45
β-strand	724-731	8	60
β-strand	736-737	2	60
β-strand	742-746	5	60
β-strand	762-767	6	60
β-strand	773-775	3	61
β-strand	782	1	62
β-strand	785	1	62
β-strand	786-804	19	63
β-strand	809-812	4	64
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-860	25
β-strand	866-868	3	29
β-strand	878-879	2	65
β-strand	882-883	2	65
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	64
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	63
β-strand	1140-1159	20	63
β-strand	1162-1164	3	66
β-strand	1168-1172	5	66
β-strand	1175-1180	6	63
β-strand	1183-1188	6	63
β-strand	1195	1	63
β-strand	1202-1205	4	66
β-strand	1213-1214	2	66

Chain C: 42 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	67
β-strand	48	1	67
β-strand	49	1	68
β-strand	54-55	2	46
β-strand	59-67	9	69
α-helix	68-69	2
β-strand	75-76	2	70
β-strand	80-81	2	71
α-helix	88-90	3
β-strand	96-97	2	72
β-strand	101-107	7	70
β-strand	109-112	4	73
β-strand	117-120	4	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	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
α-helix	238-239	2
β-strand	240-241	2	71
β-strand	256-260	5	70
β-strand	262-270	9	69
β-strand	276-281	6	69
α-helix	286-293	8
β-strand	302-307	6	75
β-strand	316-319	4	76
α-helix	330-333	4
α-helix	338	1
β-strand	339	1	77
α-helix	340	1
β-strand	347-349	3	78
β-strand	353-354	2	79
α-helix	357-362	6
β-strand	365-368	4	80
α-helix	377-380	4
β-strand	382-383	2	79
β-strand	385-388	4	78
β-strand	389-392	4	80
α-helix	395-401	7
α-helix	409-412	4
β-strand	422	1	81
β-strand	425-427	3	80
β-strand	430	1	82
β-strand	437	1	77
α-helix	443-446	4
β-strand	459-463	5	83
β-strand	467-468	2	84
β-strand	477	1	85
α-helix	479-482	4
β-strand	487	1	86
α-helix	489-491	3
β-strand	492	1	85
β-strand	494	1	87
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-505	2	88
β-strand	515	1	86
β-strand	517-518	2	88
α-helix	524-526	3
β-strand	536-537	2	84
α-helix	549	1
β-strand	550-551	2	89
α-helix	552	1
β-strand	558	1	85
β-strand	564	1	87
β-strand	572-573	2	89
β-strand	575-579	5	83
β-strand	581-582	2	82
β-strand	585-586	2	82
β-strand	588-591	4	80
β-strand	593	1	81
β-strand	594-595	2	78
β-strand	602-604	3	79
β-strand	620-624	5	76
β-strand	627-631	5	76
β-strand	632-635	4	5
β-strand	647-649	3	5
β-strand	655-660	6	5
β-strand	665-670	6	5
α-helix	671-673	3
β-strand	676-681	6	75
β-strand	689-693	5	75
α-helix	697-703	7
β-strand	712-714	3	75
β-strand	718-721	4	75
β-strand	724-731	8	90
β-strand	736-737	2	90
β-strand	742-746	5	90
β-strand	762-767	6	90
β-strand	773-775	3	33
β-strand	782	1	91
β-strand	785	1	91
β-strand	786-804	19	92
β-strand	809-812	4	93
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	836-860	25
β-strand	866-868	3	61
β-strand	878-879	2	94
β-strand	882-883	2	94
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-922	8
α-helix	923-925	3
α-helix	934-939	6
β-strand	943-946	4	93
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	1058-1062	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	92
β-strand	1140-1158	19	92
β-strand	1159	1	95
β-strand	1162-1164	3	96
β-strand	1168-1172	5	96
β-strand	1175-1180	6	95
β-strand	1183-1188	6	95
β-strand	1195	1	95
β-strand	1202-1205	4	96
α-helix	1212	1
β-strand	1213-1214	2	96

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

Element	Residues	Length	Sheet
β-strand	149-150	2	97
α-helix	157-158	2
β-strand	159-162	4	97
β-strand	167-170	4	97
β-strand	171	1	98
β-strand	172	1	99
α-helix	178-181	4
β-strand	196-200	5	99
β-strand	209-212	4	98
β-strand	225-228	4	98
β-strand	236-240	5	99
α-helix	261-263	3
β-strand	270	1	100
β-strand	273-274	2	101
β-strand	279-281	3	101
β-strand	284-285	2	100
β-strand	290-294	5	100
α-helix	295-297	3
α-helix	305-307	3
β-strand	309-310	2	101
β-strand	328	1	102
β-strand	346-350	5	100
β-strand	351	1	102
α-helix	363-366	4
β-strand	378-381	4	103
β-strand	383	1	104
β-strand	386	1	105
β-strand	398	1	104
β-strand	401-403	3	103
α-helix	407-410	4
β-strand	425-427	3	106
β-strand	428	1	103
β-strand	439	1	105
β-strand	445-447	3	103
α-helix	449-451	3
β-strand	454-458	5	103
β-strand	467	1	107
β-strand	470	1	107
β-strand	472-474	3	106
β-strand	475-476	2	103
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, F	protein	384	Homo sapiens	O15393 (AlphaFold model)

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

>8Y1E_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, F), FASTA

>8Y1E_2 Transmembrane protease serine 2 (chains D, E, F)
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
8Y1D 2.7 Å, 2up-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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