9BT1: HCoV-HKU1 glycoprotein

Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan (UUU state). Determined by electron microscopy at 2.22 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.22 Å
Organism: Human coronavirus HKU1
Chains: 3
Atoms: 29,028
Mol. weight: 466.04 kDa
Ligands: A1AR1, NAG
Released: 14 May 2025

Explore 9BT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BT1 contains 148 α-helices and 287 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: 49 helices, 94 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	66
β-strand	25-26	2	67
α-helix	31-33	3
β-strand	34-35	2	68
α-helix	36	1
β-strand	49	1	69
β-strand	54-56	3	57
β-strand	59-68	10	70
α-helix	69	1
β-strand	75-76	2	68
β-strand	80-81	2	71
β-strand	85-86	2	67
α-helix	87-90	4
β-strand	96-97	2	72
β-strand	101-107	7	68
β-strand	109-112	4	73
β-strand	117-120	4	73
β-strand	123-126	4	72
β-strand	136-141	6	72
β-strand	145-151	7	72
β-strand	155-160	6	74
β-strand	161-162	2	71
β-strand	173-175	3	74
β-strand	183-190	8	72
β-strand	197-205	9	68
β-strand	208-214	7	68
β-strand	220	1	69
β-strand	221-227	7	68
β-strand	234-238	5	72
β-strand	240-241	2	71
β-strand	256-260	5	68
β-strand	261-270	10	70
β-strand	276-281	6	70
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	75
α-helix	308-310	3
β-strand	318-319	2	76
α-helix	325	1
β-strand	326	1	77
α-helix	329-333	5
α-helix	338	1
β-strand	339	1	78
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	77
β-strand	353-354	2	77
α-helix	356-363	8
β-strand	365-371	7	77
α-helix	375-378	4
β-strand	382-392	11	77
α-helix	393-394	2
α-helix	395-401	7
α-helix	408	1
α-helix	409-413	5
β-strand	415	1	79
β-strand	422-430	9	77
β-strand	437	1	78
α-helix	443-447	5
β-strand	459-463	5	80
β-strand	467-468	2	81
β-strand	477	1	82
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	83
α-helix	489-491	3
β-strand	492	1	82
β-strand	494	1	84
α-helix	495-496	2
β-strand	504-506	3	85
β-strand	515	1	83
β-strand	516-518	3	85
β-strand	536-537	2	81
β-strand	542	1	79
β-strand	550-551	2	86
β-strand	556	1	87
β-strand	558	1	82
β-strand	566	1	84
β-strand	569	1	87
α-helix	571-573	3
β-strand	574-575	2	86
β-strand	577-581	5	80
β-strand	583-584	2	77
β-strand	587-599	13	77
β-strand	604-606	3	77
α-helix	611-612	2
β-strand	618	1	5
β-strand	622-626	5	76
β-strand	629-633	5	76
β-strand	634-637	4	5
β-strand	649-651	3	5
β-strand	657-662	6	5
β-strand	667-672	6	5
α-helix	673-675	3
β-strand	679-683	5	75
β-strand	691-695	5	75
α-helix	699-701	3
α-helix	702-706	5
β-strand	713-715	3	75
β-strand	719-722	4	75
β-strand	725-732	8	88
β-strand	738-740	3	88
β-strand	743-747	5	88
β-strand	766-771	6	88
β-strand	777-779	3	30
β-strand	786	1	89
β-strand	789	1	89
β-strand	790-808	19	90
β-strand	813-816	4	91
α-helix	818-823	6
α-helix	827-833	7
α-helix	834-836	3
α-helix	838-866	29
β-strand	870-872	3	60
β-strand	882-883	2	92
β-strand	886-887	2	92
α-helix	889-891	3
α-helix	906-912	7
α-helix	919-927	9
α-helix	938-944	7
β-strand	947-950	4	91
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	90
β-strand	1144-1163	20	90
β-strand	1166-1168	3	93
β-strand	1172-1176	5	93
β-strand	1179-1183	5	90
β-strand	1188-1192	5	90
β-strand	1199	1	90
α-helix	1203-1205	3
β-strand	1206-1209	4	93
α-helix	1212-1213	2
β-strand	1217-1219	3	93

Chain B: 52 helices, 94 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
α-helix	31-33	3
β-strand	34-35	2	3
α-helix	36	1
β-strand	49	1	4
β-strand	54-56	3	5
β-strand	59-68	10	6
α-helix	69	1
β-strand	75-76	2	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	123-126	4	8
β-strand	136-142	7	8
β-strand	145-151	7	8
β-strand	155	1	10
β-strand	156	1	1
β-strand	161	1	7
β-strand	175	1	10
β-strand	183-190	8	8
β-strand	197-205	9	3
β-strand	208-214	7	3
α-helix	219	1
β-strand	220	1	4
β-strand	221-227	7	3
β-strand	234-238	5	8
β-strand	240-241	2	7
β-strand	256-260	5	3
β-strand	261-270	10	6
α-helix	272-274	3
β-strand	276-281	6	6
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	11
α-helix	308-310	3
β-strand	318-319	2	12
α-helix	325	1
β-strand	326	1	13
α-helix	329-333	5
α-helix	338	1
β-strand	339	1	14
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	13
β-strand	353-354	2	13
α-helix	356-363	8
β-strand	365-371	7	13
α-helix	375-377	3
β-strand	382-392	11	13
α-helix	393-394	2
α-helix	395-401	7
α-helix	408	1
α-helix	409-413	5
β-strand	415	1	15
β-strand	422-430	9	13
β-strand	437	1	14
α-helix	443-447	5
β-strand	459-463	5	16
β-strand	467-468	2	17
β-strand	477	1	18
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	19
α-helix	489-491	3
β-strand	492	1	18
β-strand	494	1	20
α-helix	495-496	2
β-strand	504-506	3	21
β-strand	515	1	19
β-strand	516-518	3	21
β-strand	536-537	2	17
α-helix	539-541	3
β-strand	542	1	15
β-strand	550-551	2	22
β-strand	556	1	23
β-strand	558	1	18
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	16
β-strand	583-584	2	13
β-strand	587-599	13	13
β-strand	604-606	3	13
β-strand	622-626	5	12
β-strand	629-633	5	12
β-strand	634-637	4	24
β-strand	649-651	3	24
β-strand	657-662	6	24
β-strand	667-672	6	24
α-helix	673-675	3
β-strand	679-683	5	11
β-strand	691-695	5	11
α-helix	699-701	3
α-helix	702-706	5
β-strand	713-715	3	11
β-strand	719-722	4	11
β-strand	725-732	8	25
β-strand	738-740	3	25
β-strand	743-747	5	25
β-strand	766-771	6	25
α-helix	776	1
β-strand	777-779	3	26
β-strand	786	1	27
β-strand	789	1	27
β-strand	790-807	18	28
β-strand	813-816	4	29
α-helix	818-823	6
α-helix	827-833	7
α-helix	834-836	3
α-helix	838-866	29
β-strand	870-872	3	30
β-strand	882-883	2	31
β-strand	886-887	2	31
α-helix	889-891	3
α-helix	906-913	8
α-helix	919-927	9
α-helix	938-944	7
β-strand	947-950	4	29
α-helix	951-952	2
α-helix	956-968	13
α-helix	983-992	10
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	28
β-strand	1144-1163	20	28
β-strand	1166-1168	3	32
β-strand	1172-1176	5	32
β-strand	1179-1183	5	28
β-strand	1188-1192	5	28
β-strand	1195-1199	5	28
α-helix	1203-1205	3
β-strand	1206-1209	4	32
α-helix	1212-1213	2
β-strand	1217-1219	3	32

Chain C: 47 helices, 99 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	33
β-strand	25-26	2	34
α-helix	31-33	3
β-strand	34-35	2	35
α-helix	36	1
β-strand	49	1	36
β-strand	54-56	3	24
β-strand	59-68	10	37
α-helix	69	1
β-strand	75-76	2	35
β-strand	80-81	2	38
β-strand	85-86	2	34
α-helix	87-90	4
β-strand	96-97	2	39
β-strand	101-107	7	35
β-strand	109-113	5	40
β-strand	116-120	5	40
β-strand	123-126	4	39
β-strand	136-141	6	39
β-strand	145-151	7	39
β-strand	155	1	41
β-strand	156	1	33
β-strand	161	1	38
β-strand	175	1	41
β-strand	183-190	8	39
β-strand	197-205	9	35
β-strand	208-214	7	35
β-strand	220	1	36
β-strand	221-227	7	35
β-strand	234-238	5	39
β-strand	240-241	2	38
β-strand	256-260	5	35
β-strand	261-270	10	37
α-helix	272-274	3
β-strand	276-281	6	37
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-306	5	42
α-helix	308-313	6
β-strand	318-319	2	43
α-helix	325	1
β-strand	326	1	44
α-helix	329-333	5
α-helix	338	1
β-strand	339	1	45
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	46
β-strand	353	1	44
β-strand	354	1	47
α-helix	356-363	8
β-strand	365-371	7	46
α-helix	375-377	3
β-strand	382-392	11	46
α-helix	393-394	2
α-helix	398-401	4
α-helix	408	1
α-helix	409-413	5
β-strand	415	1	48
β-strand	422-430	9	46
β-strand	437	1	45
α-helix	443-447	5
β-strand	459-463	5	49
β-strand	467-468	2	50
β-strand	477	1	51
α-helix	478	1
α-helix	479-484	6
β-strand	487	1	52
α-helix	489-491	3
β-strand	492	1	51
β-strand	494	1	53
α-helix	495-496	2
β-strand	504-506	3	54
β-strand	515	1	52
β-strand	516-518	3	54
β-strand	536-537	2	50
β-strand	542	1	48
β-strand	550-551	2	55
β-strand	556	1	56
β-strand	558	1	51
β-strand	566	1	53
β-strand	569	1	56
α-helix	571-573	3
β-strand	574-575	2	55
β-strand	577-581	5	49
β-strand	583-584	2	46
β-strand	587-599	13	46
β-strand	604-605	2	46
β-strand	606	1	47
β-strand	618	1	57
β-strand	622	1	58
β-strand	625-626	2	43
β-strand	629-630	2	43
β-strand	633	1	58
β-strand	634-637	4	57
β-strand	649-651	3	57
β-strand	657-662	6	57
β-strand	667-672	6	57
α-helix	673-675	3
β-strand	679-683	5	42
β-strand	691-695	5	42
α-helix	699-705	7
β-strand	713-715	3	42
β-strand	719-722	4	42
β-strand	725-732	8	59
β-strand	738-740	3	59
β-strand	743-747	5	59
β-strand	766-771	6	59
β-strand	777-779	3	60
β-strand	786	1	61
β-strand	789	1	61
β-strand	790-808	19	62
β-strand	813-816	4	63
α-helix	818-823	6
α-helix	827-834	8
α-helix	839-866	28
β-strand	870-872	3	26
β-strand	882-883	2	64
β-strand	886-887	2	64
α-helix	889-891	3
α-helix	906-912	7
α-helix	919-927	9
α-helix	938-944	7
β-strand	947-950	4	63
α-helix	951-952	2
α-helix	956-968	13
α-helix	983-992	10
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	62
β-strand	1144-1163	20	62
β-strand	1166-1168	3	65
β-strand	1172-1176	5	65
β-strand	1179-1184	6	62
β-strand	1187-1192	6	62
β-strand	1195-1199	5	62
α-helix	1203-1205	3
β-strand	1206-1209	4	65
α-helix	1212-1213	2
β-strand	1217-1219	3	65

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

>9BT1_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	30

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)
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

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