9KRA: Spike protein S1

The RBD of HKU5 complex with Pipistrellus abramus ACE2. Determined by electron microscopy at 2.8 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Bat coronavirus HKU5, Pipistrellus abramus
Chains: 2
Atoms: 6,607
Mol. weight: 118.11 kDa
Ligands: NAG
Released: 5 Nov 2025

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

Secondary structure: helices and β-sheets

9KRA contains 37 α-helices and 26 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: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	389	1
β-strand	390	1	1
α-helix	391-392	2
α-helix	401-403	3
β-strand	408-409	2	2
β-strand	412	1	2
β-strand	416-417	2	1
α-helix	419-422	4
β-strand	431-434	4	2
α-helix	440-442	3
β-strand	446	1	3
β-strand	448-455	8	2
α-helix	458-460	3
β-strand	478	1	4
β-strand	485-489	5	2
β-strand	504-514	11	5
β-strand	519-521	3	5
β-strand	526	1	4
α-helix	533-536	4
β-strand	546-549	4	5
β-strand	552-560	9	5
β-strand	567-574	8	2
β-strand	582	1	3
β-strand	583-584	2	1

Chain B: 30 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	21-51	31
α-helix	61-79	19
α-helix	80-82	3
α-helix	91-101	11
α-helix	110-128	19
β-strand	132-133	2	6
β-strand	141-142	2	6
α-helix	144-150	7
α-helix	157-170	14
α-helix	176-190	15
α-helix	198-203	6
β-strand	208	1	7
β-strand	216	1	7
α-helix	221-250	30
α-helix	260	1
β-strand	261-262	2	8
α-helix	275-277	3
α-helix	293-298	6
α-helix	303-316	14
α-helix	319-323	5
β-strand	331	1	9
β-strand	346-351	6	9
β-strand	354-358	5	9
α-helix	366-381	16
α-helix	414-417	4
α-helix	431-445	15
α-helix	449-464	16
α-helix	476-479	4
α-helix	480-484	5
β-strand	486-487	2	8
α-helix	499-501	3
α-helix	503-506	4
α-helix	512-514	3
α-helix	519-528	10
α-helix	538-540	3
α-helix	547-557	11
α-helix	565-573	9
α-helix	583-586	4
α-helix	588-598	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	199	Bat coronavirus HKU5	A3EXD0 (AlphaFold model)
Angiotensin-converting enzyme	B	protein	803	Pipistrellus abramus	C7ECT9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KRA_1 Spike protein S1 (chains A)
TQECDFTPMLTGTPPPIYNFKRLVFTNCNYNLTKLLSLFQVSEFSCHQVSPSSLATGCYS
SLTVDYFAYSTDMSSYLQPGSAGAIVQFNYKQDFSNPTCRVLATVPQNLTTITKPSNYAY
LTECYKTSAYGKNYLYNAPGAYTPCLSLASRGFSTKYQSHSDGELTTTGYIYPVTGNLQM
AFIISVQYGTDTNSVCPMQ

Sequence of entity 2 (B), FASTA

>9KRA_2 Angiotensin-converting enzyme (chains B)
MSSSSWLLLSLVAVAGAQYTTEEEARRFLVKFNHEAENLSHESALASWDYNTNITDENAK
KMNEADNKWSDFYKEQSKIAQGFPLQEIKDPIIKLQLQILQQNGSSVLTAEKRKRLSTIL
TTMSTIYSTGKVCNPNNPQQCFTLSGLEDIMEKSKDYHERLWVWEGWRSEVGKQLRPLYE
EYVELKNEMARGNNYKDYGDYWRGDYETEGEKGYNYSRNYLMEDVDRIFLEIKPLYEQLH
AYVRAKLMKAYPSHISPTGCLPAHLLGDMWGRFWTNLYNLTVPLEKEPNIDVTDTMKKQS
WDAEKIFKEAEKFYSSVGLPNMTPGFWRDSMLTEPSDGRQVVCHPTAWDLGKNDFRIKMC
TKVTMDDFLTAHHEMGHIQYDMAYANQSYLLRNGANEGFHEAVGEVMSLSVATPKHLKGM
GLLPSDFSENNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFEGKIPKEQWMEKWWEMK
REIVGVVEPLPHDETYCDPASLFHVANDYSFIRYFTRTILEFQFQEALCRTAKHQGPLHK
CDISNSTEAGKKLNDMLKLGKSTPWTYALEKIAETKEMDAKPLLNYFNPLFRWLKEQNGN
SVGWSVDSSPYSNQSIKVRISLKSALGEKAYEWNENEMYLFQSSVAYAMRVYFLKAKNES
IPFRAEDVRVSDEKKRVSFKFFVTSPTNMSDIIPRSEVEDAIRMSRSRINDAFRLDDNTL
EFLGVQPTLGPPYQPPVTIWLIVFGVVMGVVVIGIGVLIFTGIRDRKKRNQAENEENPYS
SVNLSKGENNPGFQSGDDVQTSF

Ligands and cofactors

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

Browse structure collections

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