9BSW: HCoV-HKU1 Spike glycoprotein

Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDA state). Determined by electron microscopy at 2.06 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.06 Å
Organism: Human coronavirus HKU1
Chains: 3
Atoms: 29,387
Mol. weight: 471.57 kDa
Ligands: NAG
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9BSW contains 156 α-helices and 276 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: 52 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
α-helix	32-34	3
β-strand	37-39	3	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	109-113	5	9
β-strand	116-120	5	9
β-strand	124-127	4	8
β-strand	136-141	6	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
β-strand	234-237	4	8
α-helix	238-239	2
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	286-293	8
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	315-319	5	13
α-helix	324-325	2
β-strand	326	1	14
α-helix	329-333	5
β-strand	337-339	3	15
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	14
β-strand	353-354	2	14
α-helix	356-362	7
β-strand	365-371	7	14
α-helix	375-378	4
β-strand	382-392	11	14
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	16
β-strand	422-430	9	14
α-helix	431-433	3
β-strand	435-437	3	15
α-helix	443-447	5
β-strand	459-463	5	17
β-strand	467-468	2	18
β-strand	477	1	19
α-helix	478	1
α-helix	479-483	5
α-helix	489-491	3
β-strand	492	1	19
β-strand	494	1	20
α-helix	495-496	2
α-helix	500-503	4
β-strand	504-506	3	21
β-strand	516-518	3	21
β-strand	536-537	2	18
β-strand	542	1	16
α-helix	544-546	3
β-strand	550-551	2	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	574-575	2	22
β-strand	577-581	5	17
β-strand	583-584	2	14
β-strand	587-599	13	14
β-strand	604-606	3	14
α-helix	611-613	3
β-strand	621-626	6	13
β-strand	629-638	10	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	24
β-strand	738-740	3	24
β-strand	743-747	5	24
β-strand	766-771	6	24
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	928-930	3
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: 53 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	32
β-strand	25-26	2	33
α-helix	34	1
β-strand	35-39	5	34
β-strand	49	1	35
β-strand	54-56	3	13
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
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	282-284	3
α-helix	286-294	9
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	44
β-strand	353-354	2	44
α-helix	356-362	7
β-strand	365-371	7	44
α-helix	375-378	4
β-strand	382-392	11	44
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	422-430	9	44
β-strand	435-437	3	45
α-helix	443-447	5
β-strand	459-463	5	46
β-strand	466-468	3	47
β-strand	477	1	48
α-helix	478	1
α-helix	479-482	4
β-strand	487	1	49
α-helix	489-491	3
β-strand	492	1	48
β-strand	494	1	50
α-helix	495-496	2
α-helix	499-503	5
β-strand	504-509	6	49
β-strand	512-518	7	49
β-strand	536-538	3	47
α-helix	539-541	3
β-strand	550-551	2	51
α-helix	553-555	3
β-strand	556	1	52
β-strand	558	1	48
β-strand	566	1	50
β-strand	569	1	52
α-helix	571-573	3
β-strand	574-575	2	51
β-strand	577-581	5	46
β-strand	583-584	2	44
β-strand	587-599	13	44
β-strand	604-606	3	44
α-helix	611-613	3
β-strand	618	1	43
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	699-705	7
β-strand	713-716	4	41
β-strand	719-722	4	41
β-strand	724-732	9	53
β-strand	738-740	3	53
β-strand	743-747	5	53
β-strand	766-771	6	53
α-helix	776	1
β-strand	777-779	3	54
β-strand	786	1	55
β-strand	789	1	55
β-strand	790-808	19	56
β-strand	813-816	4	57
α-helix	818-822	5
α-helix	827-834	8
α-helix	837-866	30
β-strand	870-872	3	25
β-strand	882-883	2	58
β-strand	886-887	2	58
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	57
α-helix	951-952	2
α-helix	956-968	13
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	1062-1066	5
α-helix	1071-1113	43
α-helix	1114-1118	5
β-strand	1132-1141	10	56
β-strand	1144-1163	20	56
β-strand	1166-1168	3	59
β-strand	1172-1176	5	59
β-strand	1179-1183	5	56
β-strand	1188-1192	5	56
β-strand	1199	1	56
β-strand	1206-1209	4	59
α-helix	1212-1213	2
α-helix	1216	1
β-strand	1217-1219	3	59

Chain C: 51 helices, 92 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	60
β-strand	25-26	2	61
α-helix	31-34	4
β-strand	37-39	3	62
β-strand	49	1	63
β-strand	54-56	3	43
β-strand	59-67	9	64
α-helix	68-69	2
β-strand	73-76	4	62
β-strand	80-81	2	65
β-strand	85-86	2	61
α-helix	87-90	4
β-strand	96-97	2	66
β-strand	101-107	7	62
β-strand	109-113	5	67
β-strand	116-120	5	67
β-strand	124-127	4	66
β-strand	136-141	6	66
β-strand	145-151	7	66
β-strand	155-160	6	68
β-strand	161-162	2	65
β-strand	173-175	3	68
α-helix	180-182	3
β-strand	183-190	8	66
β-strand	197-205	9	62
β-strand	208-214	7	62
β-strand	220	1	63
β-strand	221-227	7	62
β-strand	234-237	4	66
β-strand	240-241	2	65
β-strand	256-260	5	62
β-strand	262-270	9	64
β-strand	276-281	6	64
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	69
α-helix	306-308	3
β-strand	309-310	2	70
α-helix	311-313	3
β-strand	315-319	5	5
α-helix	324-325	2
β-strand	326	1	71
α-helix	329-333	5
β-strand	337-339	3	72
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	71
β-strand	353-354	2	71
α-helix	356-362	7
β-strand	365-371	7	71
α-helix	375-378	4
β-strand	382-392	11	71
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	422-430	9	71
β-strand	435-437	3	72
α-helix	443-447	5
β-strand	459-463	5	73
β-strand	466-468	3	74
β-strand	477	1	75
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	76
α-helix	489-491	3
β-strand	492	1	75
β-strand	494	1	77
α-helix	495-496	2
α-helix	501-503	3
β-strand	504-509	6	76
β-strand	512-518	7	76
β-strand	536-538	3	74
α-helix	539-541	3
β-strand	550-551	2	78
α-helix	553-555	3
β-strand	556	1	79
β-strand	558	1	75
β-strand	566	1	77
β-strand	569	1	79
α-helix	571-573	3
β-strand	574-575	2	78
β-strand	577-581	5	73
β-strand	583-584	2	71
β-strand	587-599	13	71
β-strand	604-606	3	71
α-helix	612-615	4
β-strand	618	1	5
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	70
β-strand	680-683	4	69
β-strand	691-695	5	69
α-helix	699-705	7
β-strand	713-716	4	69
β-strand	719-722	4	69
β-strand	724-732	9	80
β-strand	737-740	4	80
β-strand	743-747	5	80
β-strand	766-771	6	80
β-strand	777-779	3	29
β-strand	786	1	81
β-strand	789	1	81
β-strand	790-808	19	82
β-strand	813-816	4	83
α-helix	818-823	6
α-helix	827-834	8
α-helix	838-866	29
β-strand	870-872	3	54
β-strand	882-883	2	84
β-strand	886-887	2	84
α-helix	889-891	3
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	83
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	82
β-strand	1144-1163	20	82
β-strand	1166-1168	3	85
β-strand	1172-1176	5	85
β-strand	1179-1184	6	82
β-strand	1187-1192	6	82
β-strand	1195-1200	6	82
α-helix	1203-1205	3
β-strand	1206-1209	4	85
α-helix	1212-1213	2
α-helix	1216	1
β-strand	1217-1219	3	85

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

>9BSW_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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	36

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)
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…
9IZN 2.4 Å, Crystal structure of HKU1A RBD bound to TMPRSS2

Browse structure collections

About this viewer

MolViewer shows 9BSW 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.