9EH8: Prefusion HKU5-19s Spike trimer

Structure of the prefusion HKU5-19s Spike trimer (conformation 2). Determined by electron microscopy at 2.0 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 2.0 Å
Organism: Pipistrellus bat coronavirus HKU5
Chains: 3
Atoms: 29,118
Mol. weight: 480.25 kDa
Ligands: EIC, FOL, NAG
Released: 26 Feb 2025

Explore 9EH8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EH8 contains 156 α-helices and 240 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.

Chains A, B and C: 52 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	29-30	2
α-helix	34-36	3
β-strand	37-39	3	1
α-helix	41-43	3
α-helix	47-49	3
α-helix	57-59	3
α-helix	63	1
β-strand	64	1	2
α-helix	65-66	2
β-strand	70-71	2	3
β-strand	75-82	8	4
α-helix	83-84	2
β-strand	90-92	3	5
β-strand	95-96	2	6
α-helix	97-98	2
β-strand	99-100	2	7
β-strand	103-104	2	7
β-strand	107-109	3	1
α-helix	112-114	3
β-strand	117-118	2	8
β-strand	123-127	5	5
β-strand	134-137	4	9
β-strand	140-146	7	9
β-strand	147-148	2	10
β-strand	154-157	4	8
β-strand	160-163	4	11
β-strand	168-172	5	11
β-strand	175-182	8	8
β-strand	187-197	11	8
β-strand	214	1	12
α-helix	232-240	9
β-strand	241-244	4	8
β-strand	249-253	5	8
β-strand	261-268	8	5
β-strand	271-276	6	5
β-strand	287	1	2
β-strand	288-293	6	5
α-helix	298-299	2
β-strand	301-304	4	8
β-strand	307	1	12
β-strand	308-309	2	6
β-strand	318-319	2	10
β-strand	322-326	5	5
β-strand	328-336	9	4
β-strand	342-347	6	4
α-helix	352-360	9
β-strand	368-372	5	13
α-helix	373-376	4
β-strand	382-385	4	14
β-strand	390-391	2	15
α-helix	395-398	4
β-strand	399-400	2	16
α-helix	402-404	3
α-helix	405-407	3
β-strand	409-413	5	17
β-strand	416-418	3	15
α-helix	420-424	5
β-strand	428-435	8	17
α-helix	439-444	6
β-strand	447	1	15
β-strand	449-456	8	17
α-helix	459-465	7
α-helix	472-476	5
β-strand	486-492	7	17
β-strand	499-500	2	16
β-strand	505-514	10	18
β-strand	521-522	2	18
α-helix	524-526	3
α-helix	534-537	4
β-strand	546-549	4	18
β-strand	553-561	9	18
β-strand	567-575	9	17
β-strand	583-585	3	15
α-helix	586-588	3
β-strand	602-607	6	14
β-strand	610-619	10	14
α-helix	625-627	3
β-strand	629-631	3	14
β-strand	637-641	5	14
β-strand	647-651	5	14
β-strand	658-663	6	13
β-strand	668-674	7	13
α-helix	678-686	9
α-helix	702-704	3
β-strand	705-707	3	13
β-strand	710-713	4	13
β-strand	715-722	8	19
β-strand	727-730	4	19
β-strand	733-736	4	19
α-helix	737-739	3
β-strand	755-760	6	19
β-strand	767	1	20
α-helix	769-771	3
β-strand	776-794	19	21
β-strand	800-802	3	22
α-helix	804-809	6
α-helix	813-819	7
α-helix	820-822	3
α-helix	823-848	26
α-helix	849-853	5
β-strand	856	1	23
α-helix	858-860	3
β-strand	863-864	2	24
β-strand	867-868	2	24
α-helix	870-872	3
α-helix	881-883	3
α-helix	887-894	8
α-helix	906-911	6
α-helix	925-928	4
β-strand	930-932	3	22
α-helix	933-935	3
α-helix	939-950	12
β-strand	965-966	2	25
α-helix	970-980	11
α-helix	985-990	6
α-helix	992-1004	13
α-helix	1007-1009	3
α-helix	1015-1036	22
α-helix	1037-1039	3
α-helix	1049-1055	7
α-helix	1060-1100	41
α-helix	1101-1105	5
β-strand	1119-1128	10	21
β-strand	1131-1150	20	21
β-strand	1153-1154	2	26
β-strand	1162-1165	4	26
β-strand	1168-1172	5	21
β-strand	1186-1190	5	21
β-strand	1193-1197	5	21
β-strand	1204-1207	4	26
β-strand	1214-1215	2	26
α-helix	1222-1224	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A, B, C	protein	1365	Pipistrellus bat coronavirus HKU5	A3EXD0 (AlphaFold model)

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

>9EH8_1 Spike glycoprotein (chains A, B, C)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGTQSVDMGTTGSGNCIESQVQPDFFETARN
TWPLSIDTSKAEGVIYPNGKSYSNITLTYTGLYPKANDLGKQYVFSDGHSSPGTLSRLFV
SNYSRQVEPFDSGFVVRIGAAANKTGTTIISQSTNRPIKKIYPAFMLGHSVGNYTPTNIT
GRYLNHTLVILPDGCGTLVHAFYCILQPRTQAYCAGASTFTSVTVWDTPASDCANSQSYN
RLANLNAFKLYFDLINCTFRYNYTITEDENAEWFGITQDTQGVHLYSSRKENVFRNNMFH
FATLPVYQKILYYTVIPRSIRSPFNDRKAWAAFYIYKLHPLTYLLNFDVEGYITKAVDCG
YDDLAQLQCSYQSFDVETGVYSVSSFEASPRGEFIEQATTQECDFTPMLTGTPPPIYNFK
RLVFTNCNYNLTKLLSLFQVSEFSCHQVSPSSLATGCYSSLTVDYFAYSTDMSSYLQPGS
AGEIVQFNYKQDFSNPTCRVLATVPQNLTTITKPSNYAYLTECYKTSAYGKNYLYNAPGG
YTPCLSLASRGFSTKYQSHSDGELTTTGYIYPVTGNLQMAFIISVQYGTDTNSVCPMQAL
RNDTSIEDKLDVCVEYSLHGITGRGVFHNCTSVGLRNQRFVYDTFDNLVGYHSYNGNYYC
VRPCVSVPVSVIYDKVSNSHATLFGSVACSHVTTMMSQFSRMTKTNLLARTTPGPLQTVV
GCAMGFINTSMVVDECQLPLGQSLCAIPPNPSARLARASSGVTDVFQIATLNFTSPLTLA
PINSTGFVVAVPTNFTFGVTQEYIETTIQKITVDCKQYVCNGFKKCEELLTEYGQFCSKI
NQALHGANLRQDESIANLFSSIKTQNTQPLQAGLNGDFNLTMLQIPQVTTGERKYRSAIE
DLLFNKVTIADPGYMQGYDECMQQGPQSARDLICAQYVAGYKVLPPLYDPYMEAAYTSSL
LGSIAGASWTAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKIIANKFNQALGAMQTG
FTTTNLAFNKVQDAVNANAMALSKLAAELSNTFGAISSSISDILARLDPPEQEAQIDRLI
NGRLTSLNAFVAQQLVRTEAAARSAQLAQDKVNECVKSQSKRNGFCGTGTHIVSFAINAP
NGLYFFHVGYQPTSHVNATAAYGLCNTENPPKCIAPIGGYFVLNQTTSTVANSEQQWYYT
GSSFFHPEPITEVNSKYVSMDVKFENLTNKLPPPLLSNTTDLDFKEELEEFFKNVSSQGP
NFQEISKINTTLLNLNTELMVLSEVVKQLNESYIDLKELGNYTFYQKGSGYIPEAPRDGQ
AYVRKDGEWVLLSTFLGGSGLNDIFEAQKIEWHEGGSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
EIC	Linoleic acid	C18 H32 O2	3
FOL	Folic acid	C19 H19 N7 O6	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

Molecular basis of convergent evolution of ACE2 receptor utilization among HKU5 coronaviruses. Park, Y.J., Liu, C., Lee, J. et al. Cell (2025) 188:1711-1728.e21. DOI 10.1016/j.cell.2024.12.032 · PubMed

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)
5XGR 2.1 Å, Structure of the S1 subunit C-terminal domain from bat-derived coronavirus HKU5 spike…
9KR8 2.39 Å, Overall structure of HKU5 S protein in closed conformation
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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