8Y89: Spike glycoprotein

Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2. Determined by electron microscopy at 3.32 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.32 Å
Organisms: Human coronavirus HKU1, Homo sapiens
Chains: 5
Atoms: 30,645
Mol. weight: 513 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y89 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y89 contains 119 α-helices and 298 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: 31 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	35	1	2
β-strand	54-55	2	3
β-strand	59-67	9	4
α-helix	72-74	3
β-strand	75-76	2	2
β-strand	80-81	2	5
β-strand	85-86	2	1
α-helix	88-90	3
β-strand	101-107	7	2
β-strand	109-113	5	6
β-strand	116-120	5	6
β-strand	123-127	5	7
β-strand	136-142	7	7
β-strand	145-151	7	7
β-strand	155	1	8
β-strand	175	1	8
β-strand	183-190	8	7
β-strand	197-205	9	2
β-strand	208-214	7	2
β-strand	221-227	7	2
β-strand	234-238	5	7
α-helix	239	1
β-strand	240-241	2	5
β-strand	256-260	5	2
β-strand	262-270	9	4
β-strand	276-280	5	4
α-helix	286-294	9
β-strand	302-305	4	9
β-strand	316-317	2	10
α-helix	329-333	5
β-strand	337-339	3	11
β-strand	346-349	4	12
β-strand	354	1	13
α-helix	356-362	7
β-strand	365-371	7	12
β-strand	382-392	11	12
α-helix	398-401	4
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	12
β-strand	435-437	3	11
α-helix	443-447	5
β-strand	459-462	4	14
β-strand	467	1	15
β-strand	537	1	15
β-strand	548	1	15
β-strand	576-579	4	14
β-strand	581-582	2	12
β-strand	585-597	13	12
β-strand	602-603	2	12
β-strand	604	1	13
β-strand	621-623	3	10
β-strand	628-629	2	10
β-strand	632-635	4	16
β-strand	647-648	2	16
β-strand	657-659	3	16
β-strand	666-670	5	16
α-helix	671-673	3
β-strand	678-681	4	9
β-strand	689-691	3	9
α-helix	697-699	3
α-helix	700-704	5
α-helix	708-709	2
β-strand	712-713	2	9
α-helix	719	1
β-strand	720-721	2	9
β-strand	724-731	8	17
β-strand	737	1	17
β-strand	742-746	5	17
β-strand	762-767	6	17
α-helix	772	1
β-strand	773-775	3	18
β-strand	782	1	19
β-strand	785	1	19
β-strand	786-795	10	20
β-strand	798-803	6	21
β-strand	809-811	3	22
α-helix	824-829	6
α-helix	830-832	3
α-helix	833-861	29
β-strand	866-868	3	23
β-strand	878	1	24
β-strand	883	1	24
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-941	8
β-strand	944-946	3	22
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1018	18
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1059-1062	4
α-helix	1067-1113	47
β-strand	1129-1137	9	21
β-strand	1140-1147	8	21
β-strand	1149-1158	10	20
β-strand	1159	1	25
β-strand	1162-1163	2	26
β-strand	1169-1172	4	26
β-strand	1175-1179	5	25
β-strand	1184-1188	5	25
β-strand	1195	1	25
α-helix	1199-1201	3
β-strand	1202-1205	4	26
β-strand	1213-1214	2	26

Chain B: 41 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	57
α-helix	32-34	3
β-strand	35	1	58
α-helix	38-40	3
β-strand	49	1	59
β-strand	55	1	49
β-strand	62-68	7	60
α-helix	69	1
β-strand	75-76	2	58
β-strand	85	1	57
α-helix	87-90	4
β-strand	96-97	2	61
β-strand	101-107	7	58
β-strand	109-113	5	62
β-strand	116-120	5	62
β-strand	123-127	5	61
β-strand	136-142	7	61
β-strand	145-151	7	61
β-strand	155-160	6	63
β-strand	161	1	64
β-strand	173-175	3	63
β-strand	183-190	8	61
β-strand	197-205	9	58
β-strand	208-214	7	58
β-strand	220	1	59
β-strand	221-227	7	58
β-strand	234-238	5	61
β-strand	240	1	64
β-strand	256-260	5	58
β-strand	261-267	7	60
β-strand	270	1	65
β-strand	276	1	65
β-strand	280-281	2	60
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	66
α-helix	311-313	3
β-strand	317-319	3	67
α-helix	325	1
β-strand	326	1	68
α-helix	329-333	5
β-strand	337-339	3	69
β-strand	346-350	5	70
β-strand	353-354	2	68
α-helix	357-361	5
β-strand	364-371	8	70
α-helix	375-378	4
β-strand	382-383	2	68
β-strand	385-392	8	70
α-helix	398-401	4
α-helix	409-413	5
β-strand	422-430	9	70
β-strand	435-437	3	69
α-helix	446-448	3
β-strand	459-463	5	71
β-strand	467-468	2	72
α-helix	479-482	4
β-strand	487	1	73
β-strand	494	1	74
α-helix	495-496	2
β-strand	504-506	3	75
β-strand	515	1	73
β-strand	516-518	3	75
β-strand	522	1	76
β-strand	527	1	76
β-strand	536-537	2	72
β-strand	548	1	72
β-strand	550-551	2	77
α-helix	553-555	3
β-strand	564	1	74
α-helix	569-571	3
β-strand	572-573	2	77
β-strand	575-579	5	71
β-strand	582	1	70
β-strand	585-594	10	70
β-strand	602-604	3	68
β-strand	620-624	5	67
β-strand	627-631	5	67
β-strand	632-635	4	3
β-strand	647-649	3	3
β-strand	655-660	6	3
β-strand	665-670	6	3
α-helix	671-673	3
β-strand	677-681	5	66
α-helix	688	1
β-strand	689-691	3	66
α-helix	697-702	6
β-strand	712-713	2	66
β-strand	720-721	2	66
β-strand	724-731	8	78
β-strand	737	1	78
β-strand	742-746	5	78
β-strand	762-767	6	78
α-helix	772	1
β-strand	773-775	3	23
β-strand	782	1	79
β-strand	785	1	79
β-strand	786-795	10	80
β-strand	798-804	7	81
β-strand	809-811	3	82
α-helix	814-817	4
α-helix	824-829	6
α-helix	830-832	3
α-helix	837-861	25
β-strand	866-868	3	51
β-strand	878	1	83
β-strand	883	1	83
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-922	8
α-helix	924-927	4
α-helix	934-939	6
β-strand	944-946	3	82
α-helix	947-948	2
α-helix	952-965	14
α-helix	979-988	10
α-helix	994-997	4
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	81
β-strand	1140-1147	8	81
β-strand	1149-1158	10	80
β-strand	1159	1	84
β-strand	1162-1163	2	85
β-strand	1169-1172	4	85
β-strand	1175-1179	5	84
β-strand	1184-1188	5	84
β-strand	1195	1	84
β-strand	1202-1205	4	85
β-strand	1213-1214	2	85

Chain C: 36 helices, 90 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	27
β-strand	35-39	5	28
β-strand	54	1	16
β-strand	61-67	7	29
β-strand	73-75	3	28
β-strand	80-81	2	30
β-strand	85	1	27
α-helix	87-90	4
β-strand	101-107	7	28
β-strand	110-113	4	31
β-strand	116-119	4	31
β-strand	124-127	4	32
β-strand	137-142	6	32
β-strand	145-151	7	32
β-strand	155-160	6	33
β-strand	161-162	2	30
β-strand	167	1	34
α-helix	171-172	2
β-strand	173-175	3	33
β-strand	183-190	8	32
β-strand	197-205	9	28
β-strand	208-214	7	28
β-strand	221-227	7	28
β-strand	234-237	4	32
α-helix	238-239	2
β-strand	240-241	2	30
β-strand	242	1	34
β-strand	256-260	5	28
β-strand	262-268	7	29
β-strand	279-281	3	29
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-307	6	35
β-strand	316-319	4	36
α-helix	329-333	5
β-strand	337-339	3	37
α-helix	340	1
β-strand	346-349	4	38
β-strand	353-354	2	39
α-helix	356-362	7
β-strand	364-371	8	38
β-strand	382-383	2	39
β-strand	385-392	8	38
α-helix	409-413	5
β-strand	415	1	40
β-strand	422-430	9	38
β-strand	435-437	3	37
α-helix	443-447	5
β-strand	459-463	5	41
β-strand	466-468	3	42
β-strand	477	1	43
α-helix	479-482	4
β-strand	487	1	44
β-strand	492	1	43
β-strand	494	1	45
α-helix	495-496	2
β-strand	502	1	43
β-strand	504-506	3	46
β-strand	515	1	44
β-strand	516-518	3	46
β-strand	522	1	47
β-strand	527	1	47
β-strand	536-538	3	42
β-strand	542	1	40
β-strand	548	1	42
β-strand	550-551	2	48
α-helix	553-555	3
β-strand	564	1	45
α-helix	569-571	3
β-strand	572-573	2	48
β-strand	575-579	5	41
β-strand	581-582	2	38
β-strand	585-595	11	38
β-strand	602-604	3	39
α-helix	612-614	3
β-strand	621-624	4	36
β-strand	632-635	4	49
β-strand	647-648	2	49
β-strand	657-659	3	49
β-strand	666-670	5	49
α-helix	671-673	3
β-strand	676-681	6	35
α-helix	688	1
β-strand	689-691	3	35
α-helix	697-700	4
β-strand	712-713	2	35
β-strand	720-721	2	35
β-strand	724-731	8	50
β-strand	737-739	3	50
β-strand	742-746	5	50
β-strand	762-767	6	50
β-strand	773-775	3	51
β-strand	786-804	19	52
β-strand	809-811	3	53
α-helix	814-817	4
α-helix	823-829	7
α-helix	830-832	3
α-helix	836-861	26
β-strand	866-868	3	18
β-strand	878	1	54
β-strand	883	1	54
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-941	8
β-strand	944-946	3	53
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1002-1017	16
α-helix	1018-1020	3
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1062	5
α-helix	1067-1069	3
α-helix	1071-1113	43
β-strand	1129-1137	9	52
β-strand	1140-1158	19	52
β-strand	1159	1	55
β-strand	1162-1164	3	56
β-strand	1168-1172	5	56
β-strand	1175-1179	5	55
β-strand	1184-1188	5	55
β-strand	1195	1	55
β-strand	1202-1205	4	56
β-strand	1213-1214	2	56

Chain G: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	91
α-helix	262-263	2
β-strand	271-275	5	92
β-strand	278-281	4	92
β-strand	284-285	2	93
β-strand	291-293	3	93
α-helix	300-302	3
α-helix	305-307	3
β-strand	309-312	4	92
β-strand	326-327	2	92
β-strand	328-333	6	93
β-strand	338	1	94
β-strand	343	1	94
β-strand	347-351	5	93
β-strand	365	1	91
α-helix	366-368	3
β-strand	378-383	6	91
β-strand	398-404	7	91
α-helix	407-410	4
β-strand	424-427	4	91
β-strand	442-449	8	91
β-strand	452-461	10	91
β-strand	472-475	4	91
α-helix	481-491	11

Chain T: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	86
α-helix	262-263	2
β-strand	271-275	5	87
β-strand	278-281	4	87
β-strand	284	1	88
β-strand	291-293	3	88
α-helix	300-302	3
β-strand	309-312	4	87
β-strand	326-327	2	87
β-strand	328-333	6	88
β-strand	338	1	89
β-strand	343	1	89
β-strand	347-351	5	88
α-helix	365-368	4
β-strand	378-383	6	86
β-strand	398-403	6	86
β-strand	404-405	2	90
α-helix	407-410	4
β-strand	424-427	4	90
β-strand	442	1	90
β-strand	446-449	4	86
β-strand	452-455	4	86
β-strand	459	1	90
β-strand	472-475	4	90
α-helix	481-489	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1263	Human coronavirus HKU1	Q0ZME7
Transmembrane protease serine 2	G, T	protein	383	Homo sapiens	O15393 (AlphaFold model)

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

>8Y89_1 Spike glycoprotein (chains A, B, C)
VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGAN
FRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNT
SYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNV
SADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET
LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKP
VATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNL
DKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVN
VTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA
ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINE
EKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTE
ISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCY
SGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS
CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTN
FTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDIT
QLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSPLEDLLFNKVKL
SDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA
AAGVPFPLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATPSALAKIQSVV
NANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQL
SDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSF
KTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT
KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIK
SLN

Sequence of entity 2 (G, T), FASTA

>8Y89_2 Transmembrane protease serine 2 (chains G, T)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPE
WIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALM
KLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQR
CNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAY
RPGVYGNVMVFTDWIYRQMRADG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13

Primary citation

TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Wang, H., Liu, X., Zhang, X. et al. Cell (2024) 187:4261. DOI 10.1016/j.cell.2024.06.016 · PubMed

Other PDB entries of the same protein (UniProt Q0ZME7), best resolution first:

9YXW 2.6 Å, Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab
8Y8C 2.95 Å, Structure of HCoV-HKU1C spike in the inactive-closed conformation
8Y8B 3.01 Å, Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan
8Y88 3.03 Å, Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
8Y8F 3.07 Å, Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
8Y8A 3.19 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
9YGP 3.2 Å, HCoV-HKU1 C S 2P in complex with H501-018 Fab (local cryoEM)
8Y8G 3.23 Å, Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
8Y87 3.26 Å, Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
9YGN 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 1, global cryoEM)
9YGO 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 2, global cryoEM)
8Y8D 3.41 Å, Structure of HCoV-HKU1C spike in the inactive-1up conformation

Browse structure collections

About this viewer

MolViewer shows 8Y89 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.