8Y8G: Spike glycoprotein

Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation. Determined by electron microscopy at 3.23 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.23 Å
Organism: Human coronavirus HKU1 (isolate N5)
Chains: 3
Atoms: 27,828
Mol. weight: 427.44 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y8G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8G contains 104 α-helices and 264 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: 37 helices, 90 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	27
β-strand	35	1	28
β-strand	49	1	29
β-strand	54-55	2	30
β-strand	60-68	9	31
α-helix	69	1
β-strand	75-76	2	28
β-strand	80-81	2	32
β-strand	86	1	27
α-helix	87-90	4
β-strand	97	1	33
β-strand	102-107	6	28
β-strand	109-113	5	34
β-strand	116-120	5	34
β-strand	125-127	3	33
β-strand	136-142	7	33
β-strand	145-151	7	33
β-strand	160	1	35
β-strand	161	1	32
β-strand	173	1	35
β-strand	183-190	8	33
β-strand	197-204	8	28
β-strand	208-214	7	28
β-strand	220	1	29
β-strand	221-227	7	28
β-strand	234	1	33
β-strand	240-241	2	32
β-strand	246	1	36
β-strand	250	1	36
β-strand	256-260	5	28
β-strand	261-269	9	31
β-strand	270	1	37
β-strand	276	1	37
β-strand	281	1	31
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	38
α-helix	311-313	3
β-strand	316-319	4	39
α-helix	329-333	5
β-strand	337-339	3	40
β-strand	345-349	5	41
β-strand	353-354	2	42
α-helix	356-362	7
β-strand	365-371	7	41
β-strand	383-392	10	41
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	41
β-strand	435-437	3	40
α-helix	443-447	5
β-strand	460	1	43
β-strand	463	1	44
β-strand	467-468	2	45
α-helix	479-481	3
β-strand	494	1	46
α-helix	495-496	2
β-strand	536-537	2	45
β-strand	550-551	2	47
β-strand	564	1	46
α-helix	566-568	3
α-helix	569-571	3
β-strand	572-573	2	47
β-strand	575	1	44
β-strand	578	1	43
β-strand	582	1	41
β-strand	585-597	13	41
β-strand	602	1	41
β-strand	603-604	2	42
α-helix	612-614	3
β-strand	620-624	5	39
β-strand	627-631	5	39
β-strand	632-636	5	48
β-strand	647-649	3	48
β-strand	655-659	5	48
β-strand	666-670	5	48
β-strand	678-681	4	38
α-helix	688	1
β-strand	689-691	3	38
β-strand	712-713	2	38
α-helix	719	1
β-strand	720-721	2	38
β-strand	724-725	2	49
β-strand	737	1	49
β-strand	742-746	5	49
β-strand	762-766	5	49
α-helix	772	1
β-strand	773-775	3	25
β-strand	782	1	50
β-strand	785	1	50
β-strand	786-789	4	51
β-strand	794-803	10	52
β-strand	809-812	4	53
α-helix	815-818	4
α-helix	823-829	7
α-helix	830-832	3
α-helix	833-861	29
β-strand	866-868	3	54
α-helix	869-871	3
β-strand	879	1	55
β-strand	882	1	55
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	53
α-helix	952-964	13
α-helix	979-988	10
α-helix	995-999	5
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1061-1064	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	52
β-strand	1140-1150	11	52
β-strand	1155-1158	4	51
β-strand	1159	1	56
β-strand	1162-1163	2	57
β-strand	1170-1172	3	57
β-strand	1175-1180	6	56
β-strand	1183-1188	6	56
β-strand	1195	1	56
β-strand	1202-1204	3	57
α-helix	1212	1
β-strand	1213-1214	2	57

Chain B: 34 helices, 93 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	58
α-helix	43-45	3
β-strand	49	1	59
β-strand	54-55	2	19
β-strand	60-61	2	60
β-strand	64-68	5	61
β-strand	75-76	2	62
β-strand	80-81	2	63
β-strand	85-86	2	58
β-strand	96-97	2	64
β-strand	101-107	7	62
β-strand	109-113	5	65
β-strand	116-120	5	65
β-strand	123-127	5	64
β-strand	136-138	3	64
β-strand	141	1	64
β-strand	145-151	7	64
β-strand	155	1	66
β-strand	161-162	2	63
β-strand	175	1	66
β-strand	183-190	8	64
β-strand	197-205	9	62
β-strand	208-214	7	62
β-strand	220	1	59
β-strand	221-227	7	62
β-strand	234-238	5	64
β-strand	240-241	2	63
β-strand	256-260	5	62
β-strand	261-265	5	61
β-strand	266-267	2	67
β-strand	268-269	2	60
β-strand	270	1	68
β-strand	276	1	68
β-strand	280-281	2	67
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	69
β-strand	317-318	2	70
β-strand	326	1	71
α-helix	329-333	5
β-strand	337-339	3	72
β-strand	346-349	4	73
β-strand	353	1	71
β-strand	354	1	74
α-helix	356-362	7
β-strand	364-371	8	73
β-strand	382-383	2	75
β-strand	385-392	8	73
α-helix	398-401	4
α-helix	409-412	4
β-strand	422-430	9	73
β-strand	435-437	3	72
α-helix	443-447	5
β-strand	459-462	4	76
β-strand	466-468	3	77
α-helix	479-482	4
β-strand	487	1	78
β-strand	494	1	79
α-helix	495-496	2
β-strand	504-506	3	80
β-strand	515	1	78
β-strand	516-518	3	80
β-strand	536-538	3	77
β-strand	548	1	77
β-strand	550-551	2	81
α-helix	553-555	3
β-strand	564	1	79
α-helix	569-571	3
β-strand	572-573	2	81
β-strand	576-579	4	76
β-strand	582	1	73
β-strand	585-595	11	73
β-strand	602-603	2	75
β-strand	604	1	74
β-strand	620-623	4	70
β-strand	629-631	3	70
β-strand	632	1	82
β-strand	647-649	3	30
β-strand	655-659	5	30
β-strand	666-667	2	30
β-strand	670	1	82
β-strand	677-681	5	69
α-helix	688	1
β-strand	689-693	5	69
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	69
β-strand	718-721	4	69
β-strand	724-725	2	83
β-strand	737	1	83
β-strand	742-746	5	83
β-strand	762-766	5	83
β-strand	773-775	3	54
β-strand	786-791	6	84
β-strand	794-803	10	85
β-strand	809-811	3	86
α-helix	814-818	5
α-helix	823-829	7
α-helix	834-836	3
α-helix	838-861	24
β-strand	866-868	3	21
α-helix	879-881	3
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	944-946	3	86
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1018	18
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	1132-1137	6	85
β-strand	1140-1150	11	85
β-strand	1153-1159	7	84
β-strand	1162-1163	2	87
β-strand	1169-1172	4	87
β-strand	1175-1179	5	84
β-strand	1184-1188	5	84
β-strand	1195	1	84
β-strand	1202-1205	4	87
β-strand	1213-1214	2	87

Chain C: 33 helices, 81 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	34	1	2
β-strand	49	1	3
β-strand	60-67	8	4
α-helix	68-69	2
β-strand	75-76	2	2
β-strand	80-81	2	5
β-strand	85	1	1
α-helix	88-90	3
β-strand	97	1	6
β-strand	101-107	7	2
β-strand	109-113	5	7
β-strand	116-120	5	7
β-strand	125-127	3	6
β-strand	136-142	7	6
β-strand	145-151	7	6
β-strand	161-162	2	5
β-strand	183-190	8	6
β-strand	197-205	9	2
β-strand	208-214	7	2
β-strand	220	1	3
β-strand	221-227	7	2
β-strand	234-236	3	6
β-strand	240-241	2	5
β-strand	256-260	5	2
β-strand	262-270	9	4
β-strand	276-278	3	4
β-strand	281	1	4
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-310	9	8
α-helix	311-313	3
β-strand	316-319	4	9
β-strand	326	1	10
α-helix	329-333	5
β-strand	337-338	2	11
β-strand	345-349	5	12
β-strand	353-354	2	10
β-strand	364-371	8	12
α-helix	375-377	3
β-strand	383	1	13
β-strand	385-392	8	12
α-helix	393-394	2
α-helix	398-400	3
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	12
β-strand	435-436	2	11
β-strand	460	1	14
β-strand	463	1	15
β-strand	467-468	2	16
β-strand	473	1	17
α-helix	494-496	3
β-strand	500	1	17
α-helix	501	1
β-strand	536-537	2	16
β-strand	550-551	2	18
α-helix	564-568	5
α-helix	569-571	3
β-strand	572-573	2	18
β-strand	575	1	15
β-strand	578	1	14
β-strand	581-582	2	12
β-strand	585-595	11	12
β-strand	602	1	13
β-strand	603-604	2	10
α-helix	612-615	4
β-strand	620-624	5	9
β-strand	627-631	5	9
β-strand	632-636	5	19
β-strand	647-649	3	19
β-strand	655-659	5	19
β-strand	666-670	5	19
β-strand	674-681	8	8
α-helix	688	1
β-strand	689-693	5	8
α-helix	697-703	7
β-strand	712-713	2	8
β-strand	718-721	4	8
β-strand	724-725	2	20
β-strand	737	1	20
β-strand	742-746	5	20
β-strand	762-766	5	20
β-strand	773-775	3	21
β-strand	786-791	6	22
β-strand	794-803	10	23
β-strand	809-811	3	24
α-helix	814-817	4
α-helix	823-829	7
α-helix	834-860	27
β-strand	866-868	3	25
α-helix	902-908	7
α-helix	917-923	7
α-helix	934-939	6
β-strand	944-946	3	24
α-helix	947	1
α-helix	952-964	13
α-helix	979-990	12
α-helix	994-999	6
α-helix	1001-1021	21
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	23
β-strand	1140-1150	11	23
β-strand	1153-1159	7	22
β-strand	1162-1164	3	26
β-strand	1168-1172	5	26
β-strand	1175-1179	5	22
β-strand	1184-1188	5	22
β-strand	1195	1	22
β-strand	1202-1204	3	26
β-strand	1213-1214	2	26

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

>8Y8G_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	20

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)
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

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