9BSY: HCoV-HKU1 glycoprotein

Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (DAU state). Determined by electron microscopy at 2.58 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.58 Å
Organism: Human coronavirus HKU1
Chains: 3
Atoms: 29,304
Mol. weight: 470.21 kDa
Ligands: A1AR1, NAG
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9BSY contains 156 α-helices and 289 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, 98 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
α-helix	33	1
β-strand	34-39	6	3
β-strand	49	1	4
β-strand	54-56	3	5
β-strand	59-68	10	6
α-helix	69	1
β-strand	73-76	4	3
β-strand	80-81	2	7
β-strand	85-86	2	2
α-helix	87-90	4
β-strand	96-97	2	8
β-strand	101-107	7	3
β-strand	109-112	4	9
β-strand	117-120	4	9
β-strand	124-127	4	8
β-strand	136-142	7	8
β-strand	145-151	7	8
β-strand	155-160	6	10
β-strand	161-162	2	7
β-strand	173-175	3	10
α-helix	180-182	3
β-strand	183-190	8	8
β-strand	197-205	9	3
β-strand	208-214	7	3
β-strand	220	1	4
β-strand	221-227	7	3
α-helix	231-232	2
β-strand	234-237	4	8
β-strand	240-241	2	7
β-strand	256-260	5	3
β-strand	261-270	10	6
β-strand	276-281	6	6
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	11
α-helix	306-308	3
β-strand	309-310	2	12
α-helix	311-313	3
β-strand	315	1	13
β-strand	318-319	2	14
α-helix	325	1
β-strand	326	1	15
α-helix	329-333	5
β-strand	337-339	3	16
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	15
β-strand	353-354	2	15
α-helix	356-363	8
β-strand	365-371	7	15
α-helix	375-378	4
β-strand	382-392	11	15
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	17
β-strand	422-430	9	15
β-strand	435-437	3	16
α-helix	443-447	5
β-strand	459-463	5	18
β-strand	466	1	19
β-strand	467-468	2	20
β-strand	477	1	21
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	22
α-helix	489-491	3
β-strand	492	1	21
β-strand	494	1	23
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-507	4	22
β-strand	515-518	4	22
β-strand	536-537	2	20
α-helix	539-541	3
β-strand	542	1	17
β-strand	549	1	19
β-strand	550-551	2	24
α-helix	553-555	3
β-strand	556	1	25
β-strand	558	1	21
β-strand	566	1	23
β-strand	569	1	25
β-strand	574-575	2	24
β-strand	577-581	5	18
β-strand	583-584	2	15
β-strand	587-599	13	15
β-strand	604-606	3	15
β-strand	621-622	2	13
β-strand	625-626	2	14
β-strand	629-630	2	14
β-strand	633-638	6	13
β-strand	649-651	3	13
β-strand	657-661	5	13
β-strand	668-672	5	13
α-helix	673-675	3
β-strand	676-677	2	12
β-strand	680-683	4	11
β-strand	691-695	5	11
α-helix	699-705	7
β-strand	713-716	4	11
β-strand	719-722	4	11
β-strand	724-732	9	26
β-strand	737-740	4	26
β-strand	743-747	5	26
β-strand	766-771	6	26
β-strand	777-779	3	27
β-strand	786	1	28
β-strand	789	1	28
β-strand	790-808	19	29
β-strand	813-816	4	30
α-helix	818-823	6
α-helix	827-835	9
α-helix	839-866	28
β-strand	870-872	3	31
β-strand	882-883	2	32
β-strand	886-887	2	32
α-helix	889-891	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	30
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	1062-1066	5
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	29
β-strand	1144-1163	20	29
β-strand	1166-1168	3	33
β-strand	1172-1176	5	33
β-strand	1179-1184	6	29
β-strand	1187-1192	6	29
β-strand	1195-1199	5	29
α-helix	1203-1205	3
β-strand	1206-1209	4	33
α-helix	1212-1213	2
β-strand	1217-1219	3	33

Chain B: 55 helices, 96 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	34
β-strand	25-26	2	35
α-helix	31-34	4
β-strand	35	1	36
α-helix	36	1
β-strand	49	1	37
β-strand	54-56	3	13
β-strand	59-68	10	38
α-helix	69	1
β-strand	75-76	2	36
β-strand	80-81	2	39
β-strand	85-86	2	35
α-helix	87-90	4
β-strand	96-97	2	40
β-strand	101-107	7	36
β-strand	109-113	5	41
β-strand	116-120	5	41
β-strand	123-126	4	40
β-strand	136-141	6	40
β-strand	145-151	7	40
β-strand	155-160	6	42
β-strand	161-162	2	39
α-helix	171-172	2
β-strand	173-175	3	42
β-strand	183-190	8	40
β-strand	197-205	9	36
β-strand	208-214	7	36
β-strand	220	1	37
β-strand	221-227	7	36
β-strand	234-238	5	40
α-helix	239	1
β-strand	240-241	2	39
β-strand	242	1	43
β-strand	244	1	43
β-strand	246	1	44
β-strand	250	1	44
β-strand	256-260	5	36
β-strand	261-270	10	38
α-helix	272-274	3
β-strand	276-281	6	38
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	45
α-helix	306-308	3
β-strand	309-310	2	46
α-helix	311-313	3
β-strand	315-319	5	47
α-helix	324-325	2
β-strand	326	1	48
α-helix	329-333	5
β-strand	337-339	3	49
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	48
β-strand	353-354	2	48
α-helix	356-362	7
β-strand	365-371	7	48
α-helix	375-378	4
β-strand	382-392	11	48
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	422-430	9	48
β-strand	435-437	3	49
α-helix	443-447	5
β-strand	459-463	5	50
β-strand	467-468	2	51
β-strand	477	1	52
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	53
α-helix	489-491	3
β-strand	492	1	52
β-strand	494	1	54
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-509	6	53
β-strand	512-518	7	53
β-strand	536-537	2	51
α-helix	539-541	3
β-strand	550-551	2	55
α-helix	553-555	3
β-strand	556	1	56
β-strand	558	1	52
β-strand	566	1	54
β-strand	569	1	56
α-helix	571-573	3
β-strand	574-575	2	55
β-strand	577-581	5	50
β-strand	583-584	2	48
β-strand	587-599	13	48
β-strand	604-606	3	48
α-helix	611-613	3
β-strand	618	1	47
β-strand	621-626	6	47
β-strand	629-638	10	47
β-strand	649-651	3	47
β-strand	657-661	5	47
β-strand	668-673	6	47
α-helix	674-675	2
β-strand	676-677	2	46
β-strand	680-683	4	45
β-strand	691-695	5	45
α-helix	699-705	7
β-strand	713-716	4	45
β-strand	719-722	4	45
β-strand	724-732	9	57
β-strand	738-740	3	57
β-strand	743-747	5	57
β-strand	766-771	6	57
β-strand	777-779	3	58
β-strand	786	1	59
β-strand	789	1	59
β-strand	790-808	19	60
β-strand	813-816	4	61
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	27
β-strand	882-883	2	62
β-strand	886-887	2	62
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	61
α-helix	951-952	2
α-helix	956-971	16
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	60
β-strand	1144-1163	20	60
β-strand	1166-1168	3	63
β-strand	1172-1176	5	63
β-strand	1179-1184	6	60
β-strand	1187-1192	6	60
β-strand	1199	1	60
α-helix	1203-1205	3
β-strand	1206-1209	4	63
α-helix	1212-1213	2
β-strand	1217-1219	3	63

Chain C: 53 helices, 95 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	64
β-strand	25-26	2	65
α-helix	34-36	3
β-strand	37-39	3	66
β-strand	49	1	67
β-strand	54-56	3	47
β-strand	59-68	10	68
α-helix	69	1
α-helix	72	1
β-strand	73-76	4	66
β-strand	80-81	2	69
β-strand	85-86	2	65
α-helix	87-90	4
β-strand	96-97	2	70
β-strand	101-107	7	66
β-strand	109-113	5	71
β-strand	116-120	5	71
β-strand	124-127	4	70
β-strand	136-142	7	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	66
β-strand	208-214	7	66
β-strand	220	1	67
β-strand	221-227	7	66
β-strand	234-237	4	70
β-strand	240-241	2	69
β-strand	256-260	5	66
β-strand	261-270	10	68
β-strand	276-281	6	68
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	73
α-helix	306-308	3
β-strand	309-310	2	74
α-helix	311-313	3
β-strand	315-319	5	5
α-helix	324-325	2
β-strand	326	1	75
α-helix	329-333	5
α-helix	338	1
β-strand	339	1	76
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	75
β-strand	353-354	2	75
α-helix	356-362	7
β-strand	365-371	7	75
α-helix	375-378	4
β-strand	382-392	11	75
α-helix	393-394	2
α-helix	395-401	7
α-helix	408	1
α-helix	409-413	5
β-strand	415	1	77
α-helix	416-417	2
β-strand	422-430	9	75
β-strand	437	1	76
α-helix	443-447	5
β-strand	459-463	5	78
β-strand	466	1	79
β-strand	467-468	2	80
β-strand	477	1	81
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	82
α-helix	489-491	3
β-strand	492	1	81
β-strand	494	1	83
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-509	6	82
β-strand	512-518	7	82
β-strand	536-537	2	80
β-strand	542	1	77
β-strand	549	1	79
α-helix	550	1
β-strand	551	1	84
α-helix	553-555	3
β-strand	556	1	85
β-strand	558	1	81
β-strand	566	1	83
β-strand	569	1	85
β-strand	574	1	84
β-strand	577-581	5	78
β-strand	583-584	2	75
β-strand	587-599	13	75
β-strand	604-606	3	75
β-strand	621-626	6	5
β-strand	629-638	10	5
β-strand	649-651	3	5
β-strand	657-661	5	5
β-strand	668-673	6	5
α-helix	674-675	2
β-strand	676-677	2	74
β-strand	680-683	4	73
β-strand	691-695	5	73
α-helix	699-705	7
β-strand	713-716	4	73
β-strand	719-722	4	73
β-strand	724-732	9	86
β-strand	737-740	4	86
β-strand	743-747	5	86
β-strand	766-771	6	86
β-strand	777-779	3	31
β-strand	786	1	87
β-strand	789	1	87
β-strand	790-808	19	88
β-strand	813-816	4	89
α-helix	818-823	6
α-helix	827-835	9
α-helix	839-866	28
β-strand	870-872	3	58
β-strand	882-883	2	90
β-strand	886-887	2	90
α-helix	889-891	3
α-helix	897-903	7
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	89
α-helix	951-952	2
α-helix	956-971	16
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	1062-1066	5
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	88
β-strand	1144-1163	20	88
β-strand	1166-1168	3	91
β-strand	1172-1176	5	91
β-strand	1179-1184	6	88
β-strand	1187-1192	6	88
β-strand	1195-1200	6	88
α-helix	1203-1205	3
β-strand	1206-1209	4	91
α-helix	1212-1213	2
β-strand	1217-1219	3	91

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

>9BSY_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	31

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…

Browse structure collections

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