9KR8: Spike glycoprotein

Overall structure of HKU5 S protein in closed conformation. Determined by electron microscopy at 2.39 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.39 Å
Organism: Bat coronavirus HKU5
Chains: 3
Atoms: 28,356
Mol. weight: 468.54 kDa
Ligands: PLM, NAG, OLA
Released: 5 Nov 2025

Explore 9KR8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KR8 contains 125 α-helices and 233 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: 41 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	41-44	4
α-helix	57-59	3
β-strand	63-64	2	1
α-helix	65-66	2
β-strand	70	1	2
β-strand	74-82	9	3
α-helix	83-84	2
β-strand	90-93	4	1
β-strand	117-118	2	4
β-strand	123-127	5	1
β-strand	134-135	2	5
β-strand	145-146	2	5
β-strand	147-148	2	6
β-strand	154-157	4	4
β-strand	160-162	3	7
β-strand	169-172	4	7
β-strand	175-182	8	4
β-strand	187-197	11	4
α-helix	198	1
β-strand	214	1	8
β-strand	222	1	9
β-strand	227	1	9
α-helix	231-239	9
β-strand	240-243	4	4
β-strand	248-252	5	4
β-strand	260-267	8	1
β-strand	270-276	7	1
β-strand	285-292	8	1
α-helix	297-298	2
β-strand	300-303	4	4
α-helix	304-305	2
β-strand	306	1	8
β-strand	317-318	2	6
β-strand	320-325	6	1
β-strand	327-335	9	3
β-strand	341-346	6	3
α-helix	351-359	9
β-strand	367-374	8	10
β-strand	381	1	11
β-strand	384	1	11
β-strand	390	1	12
β-strand	398-399	2	13
β-strand	408-412	5	14
β-strand	415-416	2	12
α-helix	423-425	3
β-strand	427-434	8	14
α-helix	438-441	4
β-strand	446	1	12
β-strand	448-455	8	14
α-helix	458-464	7
α-helix	471-475	5
β-strand	485-491	7	14
β-strand	498-499	2	13
α-helix	500-502	3
β-strand	504-514	11	15
β-strand	519-521	3	15
α-helix	523-525	3
α-helix	533-536	4
β-strand	545-549	5	15
β-strand	552-560	9	15
β-strand	566-574	9	14
β-strand	582-583	2	12
α-helix	585-587	3
β-strand	601-606	6	11
β-strand	609-617	9	11
β-strand	628-630	3	11
β-strand	636-640	5	11
β-strand	646-650	5	11
β-strand	655-662	8	10
β-strand	667-673	7	10
α-helix	677-679	3
β-strand	704-706	3	10
β-strand	709-712	4	10
β-strand	714-721	8	16
β-strand	727-729	3	16
β-strand	732-735	4	16
β-strand	754-759	6	16
β-strand	766	1	17
β-strand	775-793	19	18
β-strand	798-801	4	19
α-helix	803-808	6
α-helix	812-818	7
α-helix	819-821	3
α-helix	822-847	26
α-helix	848-852	5
β-strand	855	1	20
α-helix	857-859	3
β-strand	862-863	2	21
β-strand	866-867	2	21
α-helix	869-871	3
α-helix	873-874	2
α-helix	886-892	7
β-strand	899	1	22
α-helix	905-909	5
β-strand	916	1	23
β-strand	918	1	23
β-strand	920	1	22
α-helix	923-927	5
β-strand	929-932	4	19
α-helix	933-934	2
α-helix	938-950	13
β-strand	964-965	2	24
α-helix	969-978	10
α-helix	984-989	6
α-helix	991-1002	12
α-helix	1006-1008	3
α-helix	1014-1035	22
α-helix	1036-1038	3
α-helix	1048-1054	7
α-helix	1057-1099	43
α-helix	1100-1104	5
β-strand	1118-1127	10	18
β-strand	1130-1149	20	18
β-strand	1152-1153	2	25
β-strand	1161-1164	4	25
β-strand	1167-1171	5	18
β-strand	1185-1189	5	18
β-strand	1196	1	18
β-strand	1203-1206	4	25
β-strand	1213-1214	2	25
α-helix	1221-1223	3

Chain B: 41 helices, 75 β-strands

Element	Residues	Length	Sheet
α-helix	57-59	3
β-strand	63-64	2	26
α-helix	65-66	2
β-strand	70	1	27
β-strand	74-82	9	28
α-helix	83-84	2
β-strand	90-93	4	26
α-helix	112-114	3
β-strand	117-118	2	29
β-strand	123-127	5	26
β-strand	154-157	4	29
β-strand	160-162	3	30
β-strand	169-172	4	30
β-strand	175-182	8	29
β-strand	187-197	11	29
β-strand	198	1	31
β-strand	204	1	31
β-strand	214-216	3	32
β-strand	222-223	2	33
β-strand	226-227	2	33
α-helix	231-239	9
β-strand	240-252	13	29
β-strand	260-267	8	26
β-strand	270-276	7	26
β-strand	285-292	8	26
α-helix	297-298	2
β-strand	300-303	4	29
α-helix	304-305	2
β-strand	306-308	3	32
β-strand	320-325	6	26
β-strand	327-335	9	28
β-strand	341-346	6	28
α-helix	351-359	9
β-strand	367-371	5	34
β-strand	381	1	2
β-strand	384	1	2
α-helix	389	1
β-strand	390	1	35
α-helix	391	1
α-helix	394-397	4
β-strand	398-399	2	36
α-helix	401-403	3
β-strand	408-412	5	37
β-strand	415-416	2	35
β-strand	427-434	8	37
α-helix	438-441	4
β-strand	446	1	35
β-strand	448-455	8	37
α-helix	458-464	7
α-helix	471-475	5
β-strand	485-491	7	37
β-strand	498-499	2	36
α-helix	500-501	2
β-strand	504-514	11	38
β-strand	519-521	3	38
α-helix	523-525	3
α-helix	533-536	4
β-strand	545-549	5	38
β-strand	552-560	9	38
β-strand	566-574	9	37
β-strand	582-583	2	35
α-helix	585-587	3
β-strand	601-606	6	2
β-strand	609-618	10	2
β-strand	628-630	3	2
β-strand	636-640	5	2
β-strand	646-650	5	2
β-strand	657-662	6	34
β-strand	667-673	7	34
α-helix	677-680	4
β-strand	704-706	3	34
β-strand	709-712	4	34
β-strand	714-721	8	39
β-strand	727-729	3	39
β-strand	732-735	4	39
β-strand	754-759	6	39
β-strand	766	1	20
β-strand	775-793	19	24
β-strand	799-801	3	40
α-helix	803-808	6
α-helix	812-818	7
α-helix	819-821	3
α-helix	822-847	26
α-helix	848-852	5
β-strand	855	1	41
α-helix	857-859	3
β-strand	862-863	2	42
β-strand	866-867	2	42
α-helix	873-874	2
α-helix	886-892	7
β-strand	899	1	43
α-helix	905-909	5
β-strand	920	1	43
α-helix	923-927	5
β-strand	929-931	3	40
α-helix	932-934	3
α-helix	938-950	13
β-strand	964-965	2	44
α-helix	969-978	10
α-helix	984-989	6
α-helix	991-1002	12
α-helix	1005-1008	4
α-helix	1014-1035	22
α-helix	1036-1038	3
α-helix	1048-1054	7
α-helix	1057-1099	43
α-helix	1100-1104	5
β-strand	1118-1127	10	24
β-strand	1130-1149	20	24
β-strand	1152-1153	2	45
β-strand	1161-1164	4	45
β-strand	1167-1171	5	24
β-strand	1185-1189	5	24
β-strand	1192-1196	5	24
β-strand	1203-1206	4	45
β-strand	1213-1214	2	45

Chain C: 43 helices, 78 β-strands

Element	Residues	Length	Sheet
α-helix	41-43	3
α-helix	57-59	3
β-strand	63-64	2	46
α-helix	65-66	2
β-strand	70	1	11
β-strand	74-82	9	47
α-helix	83-84	2
β-strand	90-93	4	46
β-strand	99-100	2	48
β-strand	103-104	2	48
β-strand	117-118	2	49
β-strand	123-127	5	46
β-strand	135	1	50
β-strand	145	1	50
β-strand	147	1	51
β-strand	154-157	4	49
β-strand	160-162	3	52
β-strand	169-172	4	52
β-strand	175-182	8	49
β-strand	187-197	11	49
β-strand	214-216	3	53
α-helix	231-239	9
β-strand	240-243	4	49
β-strand	248-252	5	49
β-strand	260-267	8	46
β-strand	270-276	7	46
β-strand	285-292	8	46
α-helix	297-298	2
β-strand	300-303	4	49
α-helix	304-305	2
β-strand	306-308	3	53
β-strand	317	1	51
β-strand	320-325	6	46
β-strand	327-335	9	47
β-strand	341-346	6	47
α-helix	351-359	9
β-strand	367-371	5	54
α-helix	372-375	4
β-strand	381	1	27
β-strand	384	1	27
α-helix	389	1
β-strand	390	1	55
α-helix	391	1
β-strand	398-399	2	56
α-helix	401-403	3
β-strand	408-412	5	57
β-strand	415-416	2	55
α-helix	423-425	3
β-strand	427-434	8	57
α-helix	438-441	4
β-strand	446	1	55
β-strand	448-455	8	57
α-helix	458-464	7
α-helix	471-475	5
β-strand	485-491	7	57
β-strand	498-499	2	56
α-helix	500-501	2
β-strand	504-514	11	58
β-strand	519-521	3	58
α-helix	523-525	3
α-helix	533-536	4
β-strand	545-549	5	58
β-strand	552-560	9	58
β-strand	566-574	9	57
β-strand	582-583	2	55
α-helix	585-587	3
β-strand	601-606	6	27
β-strand	609-617	9	27
β-strand	628-630	3	27
β-strand	636-640	5	27
β-strand	646-650	5	27
β-strand	657-662	6	54
β-strand	667-673	7	54
β-strand	704-706	3	54
β-strand	709-712	4	54
β-strand	714-721	8	59
β-strand	727-729	3	59
β-strand	732-735	4	59
β-strand	754-759	6	59
β-strand	766	1	41
α-helix	767-770	4
β-strand	775-793	19	44
β-strand	799-801	3	60
α-helix	803-808	6
α-helix	812-818	7
α-helix	819-821	3
α-helix	822-847	26
α-helix	848-852	5
β-strand	855	1	17
β-strand	862-863	2	61
β-strand	866-867	2	61
α-helix	873-874	2
α-helix	886-892	7
β-strand	899	1	62
α-helix	905-909	5
β-strand	920	1	62
α-helix	923-927	5
β-strand	929-931	3	60
α-helix	932-934	3
α-helix	938-950	13
β-strand	964-965	2	18
α-helix	969-978	10
α-helix	984-989	6
α-helix	991-1002	12
α-helix	1005-1008	4
α-helix	1014-1035	22
α-helix	1036-1038	3
α-helix	1048-1054	7
α-helix	1057-1099	43
α-helix	1100-1104	5
β-strand	1118-1127	10	44
β-strand	1130-1149	20	44
β-strand	1152	1	63
β-strand	1161-1164	4	63
β-strand	1167-1170	4	44
β-strand	1186-1189	4	44
β-strand	1196	1	44
β-strand	1203-1206	4	63
β-strand	1213	1	63
α-helix	1214	1
α-helix	1221-1223	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1352	Bat coronavirus HKU5	A3EXD0 (AlphaFold model)

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

>9KR8_1 Spike glycoprotein (chains A, B, C)
MIRSVLVLMCSLTFIGNLTRGQSVDMGHNGTGSCLDSQVQPDYFESVHTTWPMPIDTSKA
EGVIYPNGKSYSNITLTYTGLYPKANDLGKQYLFSDGHSAPGRLNNLFVSNYSSQVESFD
DGFVVRIGAAANKTGTTVISQSTFKPIKKIYPAFLLGHSVGNYTPSNRTGRYLNHTLVIL
PDGCGTILHAFYCVLHPRTQQNCAGETNFKSLSLWDTPASDCVSGSYNQEATLGAFKVYF
DLINCTFRYNYTITEDENAEWFGITQDTQGVHLYSSRKENVFRNNMFHFATLPVYQKILY
YTVIPRSIRSPFNDRKAWAAFYIYKLHPLTYLLNFDVEGYITKAVDCGYDDLAQLQCSYE
SFEVETGVYSVSSFEASPRGEFIEQATTQECDFTPMLTGTPPPIYNFKRLVFTNCNYNLT
KLLSLFQVSEFSCHQVSPSSLATGCYSSLTVDYFAYSTDMSSYLQPGSAGAIVQFNYKQD
FSNPTCRVLATVPQNLTTITKPSNYAYLTECYKTSAYGKNYLYNAPGAYTPCLSLASRGF
STKYQSHSDGELTTTGYIYPVTGNLQMAFIISVQYGTDTNSVCPMQALRNDTSIEDKLDV
CVEYSLHGITGRGVFHNCTSVGLRNQRFVYDTFDNLVGYHSDNGNYYCVRPCVSVPVSVI
YDKASNSHATLFGSVACSHVTTMMSQFSRMTKTNLLARTTPGPLQTTVGCAMGFINSSMV
VDECQLPLGQSLCAIPPTTSSRVRRATSGASDVFQIATLNFTSPLTLAPINSTGFVVAVP
TNFTFGVTQEFIETTIQKITVDCKQYVCNGFKKCEDLLKEYGQFCSKINQALHGANLRQD
ESIANLFSSIKTQNTQPLQAGLNGDFNLTMLQIPQVTTGERKYRSTIEDLLFNKVTIADP
GYMQGYDECMQQGPQSARDLICAQYVAGYKVLPPLYDPYMEAAYTSSLLGSIAGASWTAG
LSSFAAIPFAQSIFYRLNGVGITQQVLSENQKIIANKFNQALGAMQTGFTTTNLAFNKVQ
DAVNANAMALSKLAAELSNTFGAISSSISDILARLDTVEQEAQIDRLINGRLTSLNAFVA
QQLVRTEAAARSAQLAQDKVNECVKSQSKRNGFCGTGTHIVSFAINAPNGLYFFHVGYQP
TSHVNATAAYGLCNTENPQKCIAPIDGYFVLNQTTSTVADSDQQWYYTGSSFFHPEPITE
ANSKYVSMDVKFENLTNRLPPPLLSNSTDLDFKEELEEFFKNVSSQGPNFQEISKINTTL
LNLNTELMVLSEVVKQLNESYIDLKELGNYTFYQKWPWYIWLGFIAGLVALALCVFFILC
CTGCGTSCLGKLKCNRCCDSYDEYEVEKIHVH

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33
OLA	Oleic acid	C18 H34 O2	3

Primary citation

Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5. Zhang, Y.Y., Xia, L.Y., Zhou, Q. To be published.

Other PDB entries of the same protein (UniProt A3EXD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EA0 2.0 Å, Structure of the prefusion HKU5-19s Spike trimer (conformation 1)
9EH8 2.0 Å, Structure of the prefusion HKU5-19s Spike trimer (conformation 2)
5XGR 2.1 Å, Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike…
9DAK 2.4 Å, Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2
9E0I 2.4 Å, Structure of the HKU5-19s RBD bound to the Bos taurus ACE2 receptor
9N7D 2.5 Å, Structure of the Rattus norvegicus ACE2 receptor bound HsItaly2011 RBD complex
9N7E 2.5 Å, Eptesicus fuscus ACE2 peptidase domain bound to VsCoV-a7 RBD complex
9KR9 2.8 Å, Overall structure of HKU5 S protein with S468A/Y463A mutation
9KRA 2.8 Å, The RBD of HKU5 complex with Pipistrellus abramus ACE2
9JJ6 2.94 Å, BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
9D32 3.1 Å, Structure of the HKU5 RBD bound to the P. abramus ACE2 receptor
9KRB 3.22 Å, The RBD of HKU5 complex with Pitta sordida ACE2

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