9YGN: HuCoV-HKU1 C S 2P

HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 1, global cryoEM). Determined by electron microscopy at 3.4 Å resolution. Released 1 Jul 2026.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Human coronavirus HKU1, Homo sapiens
Chains: 9
Atoms: 32,850
Mol. weight: 590.57 kDa
Ligands: NAG
Released: 1 Jul 2026

Explore 9YGN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YGN contains 125 α-helices and 345 β-strands across 9 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, 88 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
β-strand	35	1	3
β-strand	49	1	4
β-strand	64-67	4	5
α-helix	68-69	2
β-strand	75-76	2	3
β-strand	85-86	2	2
α-helix	87-90	4
β-strand	96-97	2	6
β-strand	101-107	7	3
β-strand	110-112	3	7
β-strand	117-119	3	7
β-strand	125-127	3	6
β-strand	136-142	7	6
β-strand	145-151	7	6
β-strand	155	1	8
β-strand	156	1	1
β-strand	162	1	9
β-strand	175	1	8
α-helix	180-182	3
β-strand	183-190	8	6
β-strand	197-205	9	3
β-strand	208-214	7	3
β-strand	220	1	4
β-strand	221-227	7	3
β-strand	234-235	2	6
β-strand	241	1	9
β-strand	246	1	10
β-strand	250	1	10
β-strand	256-260	5	3
β-strand	262-265	4	5
β-strand	266-267	2	11
β-strand	280-281	2	11
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	12
β-strand	318-319	2	13
β-strand	326	1	14
α-helix	329-333	5
β-strand	337-338	2	15
α-helix	341-343	3
β-strand	345-349	5	14
β-strand	353-354	2	14
α-helix	356-362	7
β-strand	364-371	8	14
α-helix	375-377	3
β-strand	382-392	11	14
α-helix	393-394	2
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	14
β-strand	435-436	2	15
α-helix	444-447	4
β-strand	459-463	5	16
β-strand	466-468	3	17
β-strand	477	1	18
α-helix	479-482	4
α-helix	489-491	3
β-strand	492	1	18
α-helix	494-496	3
β-strand	502	1	18
β-strand	504-505	2	19
β-strand	517-518	2	19
β-strand	536-538	3	17
β-strand	550-551	2	20
α-helix	553-555	3
β-strand	556	1	21
β-strand	567	1	21
α-helix	569-571	3
β-strand	572-573	2	20
β-strand	575-579	5	16
β-strand	581-582	2	14
β-strand	585-597	13	14
β-strand	602-604	3	14
α-helix	612-615	4
β-strand	620-624	5	13
β-strand	627-631	5	13
β-strand	632-633	2	22
β-strand	636	1	23
β-strand	647-649	3	23
β-strand	655-659	5	23
β-strand	666-668	3	23
β-strand	669-670	2	22
β-strand	678-681	4	12
β-strand	689-691	3	12
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	24
β-strand	720-721	2	24
β-strand	724-731	8	25
β-strand	742-746	5	25
β-strand	762-767	6	25
α-helix	772	1
β-strand	773-775	3	26
β-strand	787-791	5	27
β-strand	794-803	10	28
β-strand	811-812	2	29
α-helix	814-818	5
α-helix	823-829	7
α-helix	833-860	28
α-helix	879-881	3
α-helix	902-910	9
α-helix	915-923	9
α-helix	937-940	4
β-strand	943-944	2	29
α-helix	952-964	13
α-helix	979-989	11
α-helix	994-999	6
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1060-1064	5
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	28
β-strand	1140-1150	11	28
β-strand	1153-1157	5	27
β-strand	1158-1159	2	30
β-strand	1162-1163	2	31
β-strand	1169-1172	4	32
β-strand	1175-1180	6	30
β-strand	1183-1188	6	30
β-strand	1195	1	30
α-helix	1199-1201	3
β-strand	1202-1205	4	32
β-strand	1213-1214	2	31

Chain B: 39 helices, 91 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	33
β-strand	49	1	34
β-strand	54-55	2	23
β-strand	60-63	4	35
β-strand	80-81	2	36
β-strand	85-86	2	33
α-helix	87-90	4
β-strand	96	1	37
β-strand	101-107	7	38
β-strand	109-112	4	39
β-strand	117-120	4	39
β-strand	123-127	5	37
β-strand	137-139	3	37
β-strand	142	1	40
β-strand	145	1	40
β-strand	148-149	2	37
β-strand	160	1	41
β-strand	161-162	2	36
β-strand	173	1	41
β-strand	186-187	2	37
β-strand	190	1	40
β-strand	197-205	9	38
β-strand	208-214	7	38
β-strand	220	1	34
β-strand	221	1	38
β-strand	225-227	3	38
β-strand	234-238	5	37
β-strand	240-241	2	36
β-strand	257-260	4	38
β-strand	266-269	4	35
β-strand	270	1	42
β-strand	276	1	42
β-strand	281	1	35
α-helix	286-293	8
α-helix	299-300	2
β-strand	302-305	4	43
α-helix	306-309	4
β-strand	326	1	44
α-helix	329-333	5
β-strand	337-338	2	45
α-helix	341-343	3
β-strand	345-349	5	46
β-strand	353	1	44
α-helix	356-362	7
β-strand	364-371	8	46
α-helix	375-377	3
β-strand	383-392	10	46
α-helix	393-394	2
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	46
β-strand	435-436	2	45
α-helix	444-447	4
β-strand	459-463	5	47
β-strand	466-468	3	48
β-strand	477	1	49
α-helix	479-482	4
α-helix	489-491	3
β-strand	492	1	49
α-helix	494-496	3
β-strand	502	1	49
β-strand	504-505	2	50
β-strand	517-518	2	50
β-strand	536-538	3	48
β-strand	550-551	2	51
α-helix	553-555	3
β-strand	556	1	52
β-strand	567	1	52
α-helix	569-571	3
β-strand	572-573	2	51
β-strand	575-579	5	47
β-strand	581-582	2	46
β-strand	585-597	13	46
β-strand	602	1	46
β-strand	603	1	44
β-strand	619-624	6	53
β-strand	627-635	9	53
β-strand	648-649	2	53
β-strand	655-659	5	53
β-strand	666-670	5	53
β-strand	678-681	4	43
β-strand	689-690	2	43
α-helix	697-703	7
β-strand	714-715	2	54
β-strand	718-719	2	54
β-strand	725	1	55
β-strand	736-737	2	55
β-strand	743-746	4	55
β-strand	762-765	4	55
β-strand	786	1	56
β-strand	790-791	2	57
β-strand	795-797	3	58
β-strand	800-803	4	59
β-strand	809-812	4	60
α-helix	814-818	5
α-helix	823-827	5
α-helix	829-832	4
α-helix	833-860	28
β-strand	866-868	3	26
α-helix	869-871	3
α-helix	879-881	3
α-helix	904-910	7
α-helix	915-923	9
α-helix	934-939	6
β-strand	943-946	4	60
α-helix	947	1
α-helix	952-964	13
α-helix	979-988	10
α-helix	995-999	5
α-helix	1001-1018	18
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1058-1061	4
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1132-1136	5	59
β-strand	1141-1145	5	59
β-strand	1147-1149	3	58
α-helix	1150	1
β-strand	1153-1154	2	57
β-strand	1158	1	56
β-strand	1159	1	61
β-strand	1162-1163	2	62
β-strand	1170-1172	3	62
β-strand	1175-1180	6	61
β-strand	1183-1188	6	61
β-strand	1195	1	61
α-helix	1199-1201	3
β-strand	1202-1204	3	62
β-strand	1213-1214	2	62

Chain C: 41 helices, 88 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	63
β-strand	25-26	2	64
β-strand	35	1	65
β-strand	40	1	66
α-helix	49-51	3
β-strand	65-67	3	67
α-helix	68-69	2
β-strand	72	1	66
β-strand	75	1	65
β-strand	85-86	2	64
α-helix	87-90	4
β-strand	101-104	4	68
β-strand	111-112	2	69
β-strand	117-118	2	69
β-strand	126-127	2	70
β-strand	136-138	3	70
β-strand	145	1	71
β-strand	148-151	4	70
β-strand	155	1	72
β-strand	156	1	63
β-strand	175	1	72
α-helix	180-182	3
β-strand	183-187	5	70
β-strand	190	1	71
β-strand	199-205	7	68
β-strand	208-214	7	68
β-strand	226	1	68
β-strand	258-260	3	68
β-strand	262-264	3	67
β-strand	266-268	3	73
β-strand	279-281	3	73
α-helix	286-294	9
β-strand	306-310	5	74
α-helix	311-313	3
β-strand	316	1	75
α-helix	330-333	4
β-strand	337-338	2	76
α-helix	341-343	3
β-strand	345-349	5	77
β-strand	354	1	78
α-helix	356-362	7
β-strand	364-371	8	77
α-helix	375-377	3
β-strand	382-392	11	77
α-helix	393-394	2
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	77
β-strand	435-436	2	76
α-helix	444-447	4
β-strand	459-463	5	79
β-strand	466-468	3	80
β-strand	477	1	81
α-helix	479-482	4
α-helix	489-491	3
β-strand	492	1	81
α-helix	494-496	3
β-strand	502	1	81
β-strand	504-505	2	82
β-strand	517-518	2	82
β-strand	536-538	3	80
β-strand	550-551	2	83
α-helix	553-555	3
β-strand	556	1	84
β-strand	567	1	84
α-helix	569-571	3
β-strand	572-573	2	83
β-strand	575-579	5	79
β-strand	581-582	2	77
β-strand	585-597	13	77
β-strand	602-603	2	77
β-strand	604	1	78
β-strand	620-621	2	75
β-strand	630-631	2	75
β-strand	632-636	5	85
β-strand	648	1	85
β-strand	657-659	3	85
β-strand	666-670	5	85
β-strand	674-677	4	74
β-strand	678	1	86
β-strand	690-691	2	86
α-helix	700-704	5
β-strand	712-713	2	86
α-helix	719	1
β-strand	720-721	2	86
β-strand	724	1	87
β-strand	730	1	88
β-strand	737	1	87
β-strand	743-745	3	87
β-strand	763-765	3	87
β-strand	766	1	88
β-strand	789-791	3	89
β-strand	794-795	2	90
β-strand	801-804	4	91
β-strand	809-812	4	92
α-helix	815-818	4
α-helix	823-832	10
α-helix	834-859	26
α-helix	870-872	3
α-helix	879-881	3
α-helix	885-887	3
α-helix	902-905	4
α-helix	917-922	6
α-helix	934-940	7
β-strand	943-946	4	92
α-helix	952-964	13
α-helix	972-974	3
α-helix	979-988	10
α-helix	994-999	6
α-helix	1004-1007	4
α-helix	1010-1017	8
α-helix	1018-1020	3
α-helix	1024-1045	22
α-helix	1046-1048	3
α-helix	1061-1063	3
α-helix	1075-1108	34
β-strand	1132	1	93
β-strand	1135-1137	3	91
β-strand	1140-1143	4	91
β-strand	1145	1	93
β-strand	1149-1150	2	90
β-strand	1153-1155	3	89
β-strand	1162-1163	2	94
β-strand	1170-1172	3	94
β-strand	1175-1179	5	95
β-strand	1184-1188	5	95
β-strand	1195	1	95
β-strand	1202-1204	3	94
β-strand	1213-1214	2	94

Chains H, I and J: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	96
β-strand	11-12	2	97
β-strand	18-25	8	96
β-strand	34-39	6	98
β-strand	46-51	6	98
β-strand	57-59	3	98
β-strand	67-72	6	96
β-strand	77-82	6	96
β-strand	89-93	5	98
β-strand	94	1	99
β-strand	101	1	99
β-strand	107-108	2	98
β-strand	110-111	2	97

Chains L, M and N: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	108
β-strand	9-13	4	109
β-strand	19-24	6	108
α-helix	27-29	5
β-strand	34-38	5	109
β-strand	45-48	4	109
β-strand	49	1	110
β-strand	53	1	110
β-strand	62-67	6	108
β-strand	70-75	6	108
α-helix	80-82	3
β-strand	85-89	5	109
β-strand	90-92	3	111
β-strand	95B-97	3	111
β-strand	102-106	5	109

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1334	Human coronavirus HKU1	Q0ZME7
H501-018 Fab heavy chain	H, I, J	protein	224	Homo sapiens
H501-018 Fab light chain	L, M, N	protein	216	Homo sapiens

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

>9YGN_1 Spike glycoprotein (chains A, B, C)
MFLIIFILPTTLAVIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTT
LLFTGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSE
FSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSE
PLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPL
TCNAISSNTDNETLEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPN
TGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLL
RLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISS
SSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPS
VVNSCAKSKPPSAICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVV
GIGEHCPGLGINEEKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSG
TTCSNDLLYSNTEISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKD
FLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCV
LNAVNLTSYSVSSCDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVE
TVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNIN
SILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSR
SLLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTT
AATVAAMFPPWSAAAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFT
ATNSALAKIQSVVNANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLING
RLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYG
LLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDK
NVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLD
LYYEMNVIQESIKSLNSGRLEVLFQGPGGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH
HHHHSAWSHPQFEK

Sequence of entity 2 (H, I, J), FASTA

>9YGN_2 H501-018 Fab heavy chain (chains H, I, J)
QVQLQESGPGLVKPSETLSLTCSVSGGSISNFYWSWIRQPPGKGLEWIGYIYYTGSSEYN
PSLKSRVILSVDTSKNHFSLKLSSVTAADTAIYYCARGTWSRRLEVDLWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L, M, N), FASTA

>9YGN_3 H501-018 Fab light chain (chains L, M, N)
QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRSIQRPSGVP
DRFSGSKSGTSASLAISGLRSEDEADYYCATWDDSLNSWVFAGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

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

Primary citation

Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site. Wang, L., Joseph, J., Vasquez, S. et al. bioRxiv (2025). DOI 10.1101/2025.10.29.685445 · 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
8Y89 3.32 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
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

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