8Y8F: Spike glycoprotein

Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation. Determined by electron microscopy at 3.07 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Human coronavirus HKU1 (isolate N5)
Chains: 3
Atoms: 28,027
Mol. weight: 429.67 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8F contains 117 α-helices and 266 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: 38 helices, 87 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
β-strand	39	1	2
β-strand	49	1	3
α-helix	50-51	2
β-strand	60-68	9	4
α-helix	69	1
β-strand	73	1	2
β-strand	75-76	2	5
β-strand	80-81	2	6
β-strand	85-86	2	1
α-helix	87-90	4
β-strand	96-97	2	7
β-strand	101-107	7	5
β-strand	109-111	3	8
β-strand	118-120	3	8
β-strand	123-127	5	7
β-strand	136-142	7	7
β-strand	145-151	7	7
β-strand	155-160	6	9
β-strand	161-162	2	6
β-strand	173-175	3	9
β-strand	185-190	6	7
β-strand	197-205	9	5
β-strand	208-214	7	5
β-strand	220	1	3
β-strand	221-227	7	5
β-strand	234-238	5	7
α-helix	239	1
β-strand	240-241	2	6
β-strand	256-260	5	5
β-strand	261-270	10	4
β-strand	276-281	6	4
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-308	7	10
α-helix	311-313	3
β-strand	316-319	4	11
β-strand	326	1	12
α-helix	329-333	5
β-strand	337-339	3	13
α-helix	341-343	3
β-strand	345-349	5	12
β-strand	353-354	2	12
α-helix	356-362	7
β-strand	365-371	7	12
α-helix	375-377	3
β-strand	382-392	11	12
α-helix	399-401	3
α-helix	415-417	3
β-strand	422-430	9	12
β-strand	435-437	3	13
α-helix	443-446	4
β-strand	459-463	5	14
β-strand	466-468	3	15
β-strand	473	1	16
β-strand	477	1	17
α-helix	482-484	3
β-strand	492	1	17
α-helix	494-496	3
β-strand	500	1	16
α-helix	501-502	2
β-strand	536-538	3	15
β-strand	550-551	2	18
α-helix	569-571	3
β-strand	572-573	2	18
β-strand	575-579	5	14
β-strand	581-582	2	12
β-strand	585-597	13	12
β-strand	602-604	3	12
β-strand	616	1	19
β-strand	620-624	5	11
β-strand	627-631	5	11
β-strand	632	1	20
β-strand	633	1	19
β-strand	635	1	21
β-strand	647-649	3	21
β-strand	655-659	5	21
β-strand	666-667	2	21
β-strand	670	1	20
α-helix	671-673	3
β-strand	676-681	6	10
β-strand	689-693	5	10
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	10
β-strand	718-721	4	10
β-strand	724-731	8	22
β-strand	737-739	3	22
β-strand	742-746	5	22
β-strand	762-767	6	22
β-strand	773-775	3	23
β-strand	786-795	10	24
β-strand	798-804	7	25
β-strand	809-811	3	26
α-helix	814-818	5
α-helix	823-829	7
α-helix	836-861	26
β-strand	866-868	3	27
β-strand	878-879	2	28
β-strand	882-883	2	28
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-939	6
β-strand	944-946	3	26
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1002-1016	15
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1131-1137	7	25
β-strand	1140-1146	7	25
β-strand	1149-1159	11	24
β-strand	1162-1164	3	29
β-strand	1168-1172	5	29
β-strand	1175-1179	5	24
β-strand	1184-1188	5	24
β-strand	1195	1	24
β-strand	1202-1204	3	29
β-strand	1213-1214	2	29

Chain B: 40 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	30
β-strand	25	1	31
β-strand	39	1	32
β-strand	49	1	33
α-helix	50-51	2
β-strand	54-55	2	34
β-strand	60-67	8	35
α-helix	68-69	2
β-strand	73	1	32
β-strand	75-76	2	36
β-strand	80-81	2	37
β-strand	85	1	31
α-helix	87-90	4
β-strand	95-97	3	38
β-strand	101-107	7	36
β-strand	125-127	3	38
β-strand	136-140	5	38
β-strand	146-151	6	38
β-strand	155-160	6	39
β-strand	161	1	37
β-strand	173-175	3	39
β-strand	183-189	7	38
β-strand	197-205	9	36
β-strand	208-214	7	36
β-strand	220	1	33
β-strand	221-227	7	36
β-strand	234-236	3	38
α-helix	238-239	2
β-strand	240-241	2	37
β-strand	256-260	5	36
β-strand	262-270	9	35
β-strand	276-281	6	35
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	40
β-strand	309-310	2	41
α-helix	311-313	3
β-strand	316-319	4	42
α-helix	324-325	2
β-strand	326	1	43
α-helix	329-333	5
β-strand	337-339	3	44
β-strand	345-349	5	45
β-strand	353	1	43
β-strand	354	1	46
α-helix	357-362	6
β-strand	364-371	8	45
α-helix	375-377	3
β-strand	382-383	2	47
β-strand	385-392	8	45
α-helix	393-394	2
α-helix	398-401	4
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	45
β-strand	435-437	3	44
α-helix	443-447	5
β-strand	459-463	5	48
β-strand	467-468	2	49
β-strand	477	1	50
β-strand	492	1	50
β-strand	494	1	51
α-helix	495-496	2
β-strand	536-537	2	49
β-strand	550-551	2	52
β-strand	564	1	51
α-helix	569-571	3
β-strand	572-573	2	52
β-strand	575-579	5	48
β-strand	581-582	2	45
β-strand	585-595	11	45
β-strand	602-603	2	47
β-strand	604	1	46
α-helix	613-615	3
β-strand	620-624	5	42
β-strand	627-631	5	42
β-strand	632	1	53
β-strand	635-636	2	54
β-strand	647-648	2	54
β-strand	657-659	3	54
β-strand	666-667	2	54
β-strand	670	1	53
β-strand	674-675	2	41
β-strand	678-681	4	40
β-strand	689-693	5	40
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	40
β-strand	718-721	4	40
β-strand	724-731	8	55
β-strand	736-739	4	55
β-strand	742-746	5	55
β-strand	762-767	6	55
β-strand	773-775	3	27
β-strand	782	1	56
β-strand	785	1	56
β-strand	786-804	19	57
β-strand	809-812	4	58
α-helix	814-817	4
α-helix	823-829	7
α-helix	830-832	3
α-helix	837-861	25
β-strand	866-868	3	59
β-strand	878-879	2	60
β-strand	882-883	2	60
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	58
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	1002-1021	20
α-helix	1025-1045	21
α-helix	1046-1048	3
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	57
β-strand	1140-1158	19	57
β-strand	1159	1	61
β-strand	1162-1164	3	62
β-strand	1168-1172	5	62
β-strand	1175-1179	5	61
β-strand	1184-1188	5	61
β-strand	1195	1	61
β-strand	1202-1205	4	62
β-strand	1213-1214	2	62

Chain C: 39 helices, 88 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	63
β-strand	25-26	2	64
α-helix	31-34	4
β-strand	39	1	65
β-strand	49	1	66
β-strand	54-55	2	21
β-strand	59-68	10	67
α-helix	69	1
β-strand	73	1	65
β-strand	75-76	2	68
β-strand	80-81	2	69
β-strand	85-86	2	64
α-helix	87-90	4
β-strand	96-97	2	70
β-strand	101-107	7	68
β-strand	109-112	4	71
β-strand	117-120	4	71
β-strand	123-127	5	70
β-strand	136-141	6	70
β-strand	145-151	7	70
β-strand	155-160	6	72
β-strand	161-162	2	69
β-strand	173-175	3	72
α-helix	180-182	3
β-strand	183-190	8	70
β-strand	197-205	9	68
β-strand	208-214	7	68
β-strand	220	1	66
β-strand	221-227	7	68
β-strand	234-238	5	70
β-strand	240-241	2	69
β-strand	256-260	5	68
β-strand	261-270	10	67
β-strand	276-278	3	67
β-strand	281	1	67
α-helix	286-294	9
β-strand	302-305	4	73
β-strand	309-310	2	74
α-helix	311-313	3
β-strand	316-319	4	75
α-helix	329-333	5
β-strand	338-339	2	76
α-helix	341-343	3
β-strand	345-349	5	77
β-strand	353-354	2	78
α-helix	356-362	7
β-strand	365-371	7	77
α-helix	376-378	3
β-strand	382-383	2	78
β-strand	385-392	8	77
α-helix	409-413	5
β-strand	422-430	9	77
β-strand	436-437	2	76
α-helix	443-446	4
β-strand	459-463	5	79
β-strand	467-468	2	80
α-helix	479-482	4
α-helix	495-496	2
α-helix	500-503	4
α-helix	530-532	3
β-strand	536-537	2	80
β-strand	550-551	2	81
β-strand	556-557	2	82
β-strand	566-567	2	82
α-helix	569-571	3
β-strand	572-573	2	81
β-strand	575-579	5	79
β-strand	585-595	11	77
β-strand	602-604	3	78
α-helix	613-615	3
β-strand	621-624	4	75
β-strand	627-629	3	75
β-strand	632-636	5	83
β-strand	647-649	3	34
β-strand	655-658	4	34
β-strand	659	1	83
β-strand	666-670	5	83
β-strand	674-675	2	74
β-strand	678-681	4	73
α-helix	688	1
β-strand	689	1	73
β-strand	690-693	4	84
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	84
β-strand	718-721	4	84
β-strand	724-725	2	85
β-strand	736-739	4	85
β-strand	742-746	5	85
β-strand	762-766	5	85
β-strand	773-775	3	59
β-strand	782	1	86
β-strand	785	1	86
β-strand	786-804	19	87
β-strand	809-812	4	88
α-helix	814-818	5
α-helix	823-829	7
α-helix	835-861	27
β-strand	866-868	3	23
α-helix	873-876	4
β-strand	878-879	2	89
β-strand	882-883	2	89
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	924-926	3
α-helix	934-940	7
β-strand	943-946	4	88
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-998	5
α-helix	1001-1018	18
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1064	7
α-helix	1067-1113	47
β-strand	1129-1137	9	87
β-strand	1140-1158	19	87
β-strand	1159	1	90
β-strand	1162-1164	3	91
β-strand	1168-1172	5	91
β-strand	1175-1179	5	90
β-strand	1184-1188	5	90
β-strand	1195	1	90
β-strand	1202-1205	4	91
β-strand	1213-1214	2	91

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1263	Human coronavirus HKU1 (isolate N5)	Q0ZME7

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

>8Y8F_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

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	32

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
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
8Y89 3.32 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
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 8Y8F 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.