9BTD: HCoV-HKU1 glycoprotein

Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DDA state). Determined by electron microscopy at 2.43 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.43 Å
Organism: Human coronavirus HKU1
Chains: 3
Atoms: 29,561
Mol. weight: 474.14 kDa
Ligands: A1AR1, NAG
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9BTD contains 156 α-helices and 282 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: 48 helices, 94 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	34-36	3
β-strand	37-39	3	2
β-strand	49	1	3
β-strand	54-55	2	4
β-strand	59-68	10	5
α-helix	69	1
β-strand	73-76	4	2
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	2
β-strand	109-113	5	8
β-strand	116-120	5	8
β-strand	124-127	4	7
β-strand	136-141	6	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
α-helix	180-182	3
β-strand	183-190	8	7
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	234-237	4	7
β-strand	240-241	2	6
β-strand	256-260	5	2
β-strand	261-270	10	5
β-strand	276-281	6	5
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	10
α-helix	306-308	3
β-strand	309-310	2	11
α-helix	311-313	3
β-strand	315-319	5	12
α-helix	324-325	2
β-strand	326	1	13
α-helix	329-333	5
β-strand	337-339	3	14
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	13
β-strand	353-354	2	13
α-helix	356-362	7
β-strand	364-371	8	13
α-helix	375-378	4
β-strand	382-392	11	13
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	15
β-strand	422-430	9	13
β-strand	435-437	3	14
α-helix	443-447	5
β-strand	459-463	5	16
β-strand	467-468	2	17
β-strand	473	1	18
β-strand	477	1	19
α-helix	478	1
α-helix	479-484	6
α-helix	489-491	3
β-strand	492	1	19
β-strand	494	1	20
α-helix	495-496	2
β-strand	500	1	18
α-helix	501-503	3
β-strand	504-506	3	21
β-strand	516-518	3	21
β-strand	536-537	2	17
β-strand	542	1	15
β-strand	551	1	22
α-helix	553-555	3
β-strand	556	1	23
β-strand	558	1	19
β-strand	566	1	20
β-strand	569	1	23
α-helix	571-573	3
β-strand	574	1	22
β-strand	577-581	5	16
β-strand	583-584	2	13
β-strand	587-599	13	13
β-strand	604-606	3	13
β-strand	618	1	12
β-strand	621-626	6	12
β-strand	629-638	10	12
β-strand	649-651	3	12
β-strand	657-661	5	12
β-strand	668-672	5	12
α-helix	673-675	3
β-strand	676-677	2	11
β-strand	680-683	4	10
β-strand	691-695	5	10
α-helix	699-705	7
β-strand	713-716	4	10
β-strand	719-722	4	10
β-strand	724-732	9	24
β-strand	737-740	4	24
β-strand	743-747	5	24
β-strand	766-771	6	24
α-helix	776	1
β-strand	777-779	3	25
β-strand	786	1	26
β-strand	789	1	26
β-strand	790-808	19	27
β-strand	813-816	4	28
α-helix	818-822	5
α-helix	827-834	8
α-helix	839-866	28
β-strand	870-872	3	29
β-strand	882-883	2	30
β-strand	886-887	2	30
α-helix	889-891	3
α-helix	896-898	3
α-helix	906-912	7
α-helix	919-927	9
α-helix	938-944	7
β-strand	947-950	4	28
α-helix	951-952	2
α-helix	956-971	16
α-helix	983-992	10
α-helix	998-1003	6
α-helix	1005-1022	18
α-helix	1028-1049	22
α-helix	1050-1052	3
α-helix	1062-1068	7
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	27
β-strand	1144-1163	20	27
β-strand	1166-1168	3	31
β-strand	1172-1176	5	31
β-strand	1179-1184	6	27
β-strand	1187-1192	6	27
β-strand	1195-1199	5	27
α-helix	1203-1205	3
β-strand	1206-1209	4	31
α-helix	1212-1213	2
β-strand	1217-1219	3	31

Chain B: 57 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	32
β-strand	25-26	2	33
α-helix	33-34	2
β-strand	35-39	5	34
β-strand	49	1	35
β-strand	54-56	3	12
β-strand	59-68	10	36
α-helix	69	1
β-strand	73-76	4	34
β-strand	80-81	2	37
β-strand	85-86	2	33
α-helix	87-90	4
β-strand	96-97	2	38
β-strand	101-107	7	34
β-strand	109-113	5	39
β-strand	116-120	5	39
β-strand	124-127	4	38
β-strand	137-141	5	38
β-strand	145-150	6	38
β-strand	155-160	6	40
β-strand	161-162	2	37
α-helix	171-172	2
β-strand	173-175	3	40
α-helix	180-182	3
β-strand	185-190	6	38
β-strand	197-205	9	34
β-strand	208-214	7	34
β-strand	220	1	35
β-strand	221-227	7	34
α-helix	231-232	2
β-strand	234-237	4	38
β-strand	240-241	2	37
β-strand	256-260	5	34
β-strand	261-270	10	36
β-strand	276-281	6	36
α-helix	286-293	8
α-helix	299-300	2
β-strand	302-305	4	41
α-helix	306-308	3
β-strand	309-310	2	42
α-helix	311-313	3
β-strand	315-319	5	43
α-helix	324-325	2
β-strand	326	1	44
α-helix	329-333	5
β-strand	337-339	3	45
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	46
β-strand	353-354	2	44
α-helix	356-362	7
β-strand	365-371	7	46
α-helix	375-378	4
β-strand	382-383	2	44
β-strand	385-392	8	46
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	422-430	9	46
β-strand	435-437	3	45
α-helix	443-447	5
β-strand	459-463	5	47
β-strand	466-468	3	48
β-strand	477	1	49
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	50
α-helix	489-491	3
β-strand	492	1	49
β-strand	494	1	51
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-509	6	50
β-strand	512-518	7	50
β-strand	536-538	3	48
α-helix	539-541	3
β-strand	550-551	2	52
α-helix	553-555	3
β-strand	556	1	53
β-strand	558	1	49
β-strand	566	1	51
β-strand	569	1	53
α-helix	571-573	3
β-strand	574-575	2	52
β-strand	577-581	5	47
β-strand	583-584	2	46
β-strand	587-597	11	46
β-strand	604-606	3	44
α-helix	611-613	3
β-strand	621-626	6	43
β-strand	629-638	10	43
β-strand	649-651	3	43
β-strand	657-661	5	43
β-strand	668-672	5	43
α-helix	673-675	3
β-strand	676-677	2	42
β-strand	680-683	4	41
β-strand	691-695	5	41
α-helix	699-701	3
α-helix	702-706	5
β-strand	713-716	4	41
β-strand	719-722	4	41
β-strand	724-732	9	54
β-strand	738-740	3	54
β-strand	743-747	5	54
β-strand	766-771	6	54
α-helix	776	1
β-strand	777-779	3	55
β-strand	786	1	56
β-strand	789	1	56
β-strand	790-808	19	57
β-strand	813-816	4	58
α-helix	818-822	5
α-helix	827-833	7
α-helix	834-836	3
α-helix	837-866	30
β-strand	870-872	3	25
β-strand	882-883	2	59
β-strand	886-887	2	59
α-helix	889-891	3
α-helix	896-898	3
α-helix	906-912	7
α-helix	919-927	9
α-helix	928-930	3
α-helix	938-944	7
β-strand	947-950	4	58
α-helix	951-952	2
α-helix	956-968	13
α-helix	983-993	11
α-helix	998-1003	6
α-helix	1005-1021	17
α-helix	1022-1024	3
α-helix	1028-1049	22
α-helix	1050-1052	3
α-helix	1062-1068	7
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	57
β-strand	1144-1163	20	57
β-strand	1166-1168	3	60
β-strand	1172-1176	5	60
β-strand	1179-1184	6	57
β-strand	1187-1192	6	57
β-strand	1195-1199	5	57
α-helix	1203-1205	3
β-strand	1206-1209	4	60
α-helix	1212-1213	2
α-helix	1216	1
β-strand	1217-1218	2	60

Chain C: 51 helices, 96 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	61
β-strand	25-26	2	62
α-helix	34-36	3
β-strand	37-39	3	63
β-strand	49	1	64
β-strand	54-56	3	43
β-strand	59-68	10	65
α-helix	69	1
β-strand	73-76	4	63
β-strand	80-81	2	66
β-strand	85-86	2	62
α-helix	87-90	4
β-strand	96-97	2	67
β-strand	101-107	7	63
β-strand	109-113	5	68
β-strand	116-120	5	68
β-strand	124-127	4	67
β-strand	136-141	6	67
β-strand	145-151	7	67
β-strand	155-160	6	69
β-strand	161-162	2	66
β-strand	173-175	3	69
α-helix	180-182	3
β-strand	183-190	8	67
β-strand	197-205	9	63
β-strand	208-214	7	63
β-strand	220	1	64
β-strand	221-227	7	63
β-strand	234-237	4	67
β-strand	240-241	2	66
β-strand	256-260	5	63
β-strand	261-270	10	65
β-strand	276-281	6	65
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	70
α-helix	306-308	3
β-strand	309-310	2	71
α-helix	311-313	3
β-strand	315-319	5	4
α-helix	324-325	2
β-strand	326	1	72
α-helix	329-333	5
β-strand	337-339	3	73
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	74
β-strand	353-354	2	72
α-helix	356-362	7
β-strand	365-371	7	74
α-helix	375-378	4
β-strand	382-383	2	72
β-strand	385-392	8	74
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	75
β-strand	422-430	9	74
β-strand	435-437	3	73
α-helix	443-447	5
β-strand	459-463	5	76
β-strand	466	1	77
β-strand	467-468	2	78
β-strand	477	1	79
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	80
α-helix	489-491	3
β-strand	492	1	79
β-strand	494	1	81
α-helix	495-496	2
α-helix	501-503	3
β-strand	504-509	6	80
β-strand	512-518	7	80
β-strand	536-537	2	78
α-helix	539-541	3
β-strand	542	1	75
β-strand	549	1	77
β-strand	551	1	82
α-helix	553-555	3
β-strand	556	1	83
β-strand	558	1	79
β-strand	566	1	81
β-strand	569	1	83
α-helix	571-573	3
β-strand	574	1	82
β-strand	577-581	5	76
β-strand	583-584	2	74
β-strand	587-597	11	74
β-strand	604-606	3	72
α-helix	611-613	3
β-strand	621-626	6	4
β-strand	629-637	9	4
β-strand	649-651	3	4
β-strand	657-661	5	4
β-strand	668-672	5	4
α-helix	673-675	3
β-strand	676-677	2	71
β-strand	680-683	4	70
β-strand	691-695	5	70
α-helix	699-705	7
β-strand	713-715	3	70
β-strand	719-722	4	70
β-strand	724-732	9	84
β-strand	737-740	4	84
β-strand	743-747	5	84
β-strand	766-771	6	84
β-strand	777-779	3	29
α-helix	785	1
β-strand	786	1	85
β-strand	789	1	85
β-strand	790-808	19	86
β-strand	813-816	4	87
α-helix	818-823	6
α-helix	827-835	9
α-helix	838-866	29
β-strand	870-872	3	55
β-strand	882-883	2	88
β-strand	886-887	2	88
α-helix	897-899	3
α-helix	906-912	7
α-helix	919-927	9
α-helix	928-930	3
α-helix	938-944	7
β-strand	947-950	4	87
α-helix	951-952	2
α-helix	956-971	16
α-helix	983-993	11
α-helix	998-1003	6
α-helix	1005-1022	18
α-helix	1028-1049	22
α-helix	1050-1052	3
α-helix	1062-1068	7
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	86
β-strand	1144-1163	20	86
β-strand	1166-1168	3	89
β-strand	1172-1176	5	89
β-strand	1179-1184	6	86
β-strand	1187-1192	6	86
β-strand	1195-1199	5	86
α-helix	1203-1205	3
β-strand	1206-1209	4	89
α-helix	1212-1213	2
α-helix	1216	1
β-strand	1217-1219	3	89

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1348	Human coronavirus HKU1	Q5MQD0 (AlphaFold model)

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

>9BTD_1 Spike glycoprotein (chains A, B, C)
VIGDFNCTNFAINDLNTTVPRISEYVVDVSYGLGTYYILDRVYLNTTILFTGYFPKSGAN
FRDLSLKGTTYLSTLWYQKPFLSDFNNGIFSRVKNTKLYVNKTLYSEFSTIVIGSVFINN
SYTIVVQPHNGVLEITACQYTMCEYPHTICKSKGSSRNESWHFDKSEPLCLFKKNFTYNV
STDWLYFHFYQERGTFYAYYADSGMPTTFLFSLYLGTLLSHYYVLPLTCNAISSNTDNET
LQYWVTPLSKRQYLLKFDNRGVITNAVDCSSSFFSEIQCKTKSLLPNTGVYDLSGFTVKP
VATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNF
DESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAIN
VTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSA
SCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDE
EKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLLQPN
TEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTNKTYNIFP
CYAGRVSAAFHQNASSLALLYRNLKCSYVLNNISLTTQPYFDSYLGCVFNADNLTDYSVS
SCALRMGSGFCVDYNSPSSSSSRRKRRSISASYRFVTFEPFNVSFVNDSIESVGGLYEIK
IPTNFTIVGQEEFIQTNSPKVTIDCSLFVCSNYAACHDLLSEYGTFCDNINSILDEVNGL
LDTTQLHVADTLMQGVTLSSNLNTNLHFDVDNINFKSLVGCLGPHCGSSSRSFFEDLLFD
KVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSESQISGYTTAATVAAMFP
PWSAAAGIPFSLNVQYRINGLGVTMDVLNKNQKLIATAFNNALLSIQNGFSAPNSALAKI
QSVVNSNAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYV
SQQLSDISLVKFGAALAMEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFMHFSYK
PISFKTVLVSPGLCISGDVGIAPKQGYFIKHNDHWMFTGSSYYYPEPISDKNVVFMNTCS
VNFTKAPLVYLNHSVPKLSDFESELSHWFKNQTSIAPNLTLNLHTINATFLDLYYEMNLI
QESIKSLNNSYINLKDIGTYEMYVKSGGYIPEAPRDGQAYVRKDGEWVLLSTFLNSGRAH
HHHHHGAGGLNDIFEAQKIEWHEDTAAA

Ligands and cofactors

ID	Name	Formula	Copies
A1AR1	5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-n…	C24 H38 N2 O18	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	37

Primary citation

Human coronavirus HKU1 spike structures reveal the basis for sialoglycan specificity and carbohydrate-promoted conformational changes. Jin, M., Hassan, Z., Li, Z. et al. Nat Commun (2025) 16:4158-4158. DOI 10.1038/s41467-025-59137-y · PubMed

Other PDB entries of the same protein (UniProt Q5MQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9JCY 1.8 Å, Crystal structure of the HCoV-HKU1 RBD in complex with Fab
5KWB 1.91 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BT2 1.93 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein D1 (Down State, locally refined)
9BSW 2.06 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDA state)
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
9BT9 2.11 Å, Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined)
9BT1 2.22 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BT0 2.23 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDD state)
5GNB 2.3 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BTB 2.33 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…
9BSX 2.37 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BTA 2.39 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…

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