9JJ6: BtHKU5-CoV-2-441 Spike RBD domain

BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2. Determined by electron microscopy at 2.94 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 2.94 Å
Organisms: Pipistrellus bat coronavirus HKU5, Homo sapiens
Chains: 2
Atoms: 6,314
Mol. weight: 98.17 kDa
Ligands: NAG
Released: 12 Mar 2025

Explore 9JJ6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JJ6 contains 44 α-helices and 20 β-strands across 2 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: 37 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	21-52	32
α-helix	56-80	25
α-helix	91-100	10
α-helix	104-107	4
α-helix	110-128	19
β-strand	131-132	2	4
β-strand	142-143	2	4
α-helix	144-148	5
α-helix	149-154	6
α-helix	158-171	14
α-helix	173-175	3
α-helix	177-192	16
α-helix	199-204	6
α-helix	205-207	3
β-strand	209	1	5
β-strand	217	1	5
α-helix	221-249	29
β-strand	262-263	2	6
α-helix	264-266	3
α-helix	276-278	3
α-helix	279-282	4
α-helix	289-291	3
α-helix	294-299	6
α-helix	304-318	15
α-helix	320-324	5
α-helix	325-330	6
β-strand	347-352	6	7
β-strand	355-359	5	7
α-helix	366-385	20
α-helix	390-392	3
α-helix	400-412	13
α-helix	415-420	6
α-helix	432-445	14
α-helix	449-464	16
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	6
α-helix	500-502	3
α-helix	504-507	4
α-helix	514-532	19
α-helix	548-558	11
α-helix	566-574	9
α-helix	582-587	6
α-helix	589-598	10

Chain B: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	379-382	4
α-helix	385-387	3
β-strand	388	1	1
α-helix	389-391	3
α-helix	392	1
β-strand	393-397	5	1
α-helix	404-409	6
β-strand	411	1	2
β-strand	415-419	5	1
β-strand	433-440	8	1
α-helix	443-449	7
β-strand	470-475	6	1
β-strand	477	1	2
β-strand	489-499	11	3
β-strand	502-505	4	3
α-helix	507-509	3
β-strand	523-526	4	3
β-strand	533-541	9	3
β-strand	549-556	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BtHKU5-CoV-2-441 Spike RBD domain	B	protein	239	Pipistrellus bat coronavirus HKU5	A3EXD0 (AlphaFold model)
Processed angiotensin-converting enzyme 2	A	protein	608	Homo sapiens	Q9BYF1 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9JJ6_1 BtHKU5-CoV-2-441 Spike RBD domain (chains B)
MDAMKRGLCCVLLLCGAVFVSAAKSRGKFIEQPKVQECDFSPLLTGTPPQVYNFNRLSFT
NCNYNLTKLLSLFEVSEFSCNAISPSALASTCYSSLTVDYFAFPLSMASYLRPGSTGPTA
EFNYRQDFSNPTCRVLATPSSNITITKPSNYNWIRLCRTTGAFGNRDQKVQPGHYSRCRY
IAPTGSIYLGGNEGYLVSDGQSASMTERVQMTFVISVTFGTESNSVCPAAAHHHHHHHH

Sequence of entity 2 (A), FASTA

>9JJ6_2 Processed angiotensin-converting enzyme 2 (chains A)
STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQST
LAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNP
QECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYED
YGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISP
IGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSV
GLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGH
IQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINF
LLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYC
DPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNML
RLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADAAA
HHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Bat-infecting merbecovirus HKU5-CoV lineage 2 can use human ACE2 as a cell entry receptor. Chen, J., Zhang, W., Li, Y. et al. Cell (2025) 188:1729-1742.e16. DOI 10.1016/j.cell.2025.01.042 · 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)
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…
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
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

Browse structure collections

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