9KRB: The RBD of HKU5 complex with Pitta sordida ACE2

The RBD of HKU5 complex with Pitta sordida ACE2. Determined by electron microscopy at 3.22 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 3.22 Å
Organisms: Bat coronavirus HKU5, Pitta sordida
Chains: 2
Atoms: 6,587
Mol. weight: 113.18 kDa
Ligands: NAG
Released: 5 Nov 2025

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

Secondary structure: helices and β-sheets

9KRB contains 46 α-helices and 25 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: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	390	1	1
α-helix	394-397	4
β-strand	399	1	2
β-strand	408-409	2	3
β-strand	412	1	3
β-strand	415-417	3	1
α-helix	419-423	5
β-strand	431-434	4	3
β-strand	446	1	1
β-strand	448-455	8	3
α-helix	458-460	3
α-helix	472-475	4
β-strand	485-488	4	3
β-strand	499	1	2
β-strand	504-514	11	4
β-strand	519-521	3	4
α-helix	523-525	3
α-helix	533-536	4
β-strand	546-549	4	4
β-strand	552-560	9	4
β-strand	567-574	8	3
β-strand	582-584	3	1

Chain B: 40 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	21-34	14
α-helix	38-50	13
α-helix	56-65	10
α-helix	68-79	12
α-helix	96-99	4
α-helix	104-106	3
α-helix	111-127	17
β-strand	130-132	3	5
β-strand	140-142	3	5
α-helix	143-147	5
α-helix	148-153	6
α-helix	157-171	15
α-helix	176-189	14
α-helix	198-203	6
β-strand	208	1	6
β-strand	216	1	6
α-helix	221-232	12
α-helix	236-239	4
α-helix	243-251	9
α-helix	261	1
β-strand	262-263	2	7
α-helix	276-278	3
α-helix	289-291	3
α-helix	294-298	5
α-helix	306-310	5
α-helix	315-318	4
α-helix	321-323	3
α-helix	327-330	4
β-strand	332	1	8
β-strand	347-350	4	8
β-strand	356-359	4	8
α-helix	372-382	11
α-helix	400-403	4
α-helix	419-421	3
α-helix	433-446	14
α-helix	450-464	15
α-helix	470-472	3
α-helix	473-480	8
α-helix	481-485	5
β-strand	487-488	2	7
α-helix	499-502	4
α-helix	504-507	4
α-helix	513-515	3
α-helix	521-532	12
α-helix	539-541	3
α-helix	555-558	4
α-helix	566-571	6
α-helix	582-587	6
α-helix	589-598	10

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	770	Pitta sordida	A0A851FF99 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9KRB_1 Spike protein S1 (chains A)
TQECDFTPMLTGTPPPIYNFKRLVFTNCNYNLTKLLSLFQVSEFSCHQVSPSSLATGCYS
SLTVDYFAYSTDMSSYLQPGSAGAIVQFNYKQDFSNPTCRVLATVPQNLTTITKPSNYAY
LTECYKTSAYGKNYLYNAPGAYTPCLSLASRGFSTKYQSHSDGELTTTGYIYPVTGNLQM
AFIISVQYGTDTNSVCPMQ

Sequence of entity 2 (B), FASTA

>9KRB_2 Angiotensin-converting enzyme (chains B)
MLVHLWLLCGLSAVVTPQDIGQQAQEFLEEFNRRAEDISYESSLASWNYNTNITEENAKK
MNEAGARWSAFYDTASRNASKFPVDSIEDDLIKLQIQILQDRGSSVLTPEKYNRLGTVLS
TMSTIYSTGTVCKINNPSECLVLEPGLDAIMADSTDYHERLWAWEGWRADVGRMMRPLYE
EYVELENEVAKLNGYSDYGDYWRANYEADFPKGYEYKRDQLIEDVEKTFKQIKPLYEQLH
AYVRHQLEQVYGPELISSTGCLPAHLLGDMWGRFWTNLYALTVPYPNKPNIDVTSAMVEK
EWDANKIFRSAEAFFISIGLDNMTEGFWRDSMLTEPTDNRKVVCHPTAWDLGKNDYRIKM
CTKVTMDDFLTAHHEMGHIEYDMAYSGQPYLLRSGANEGFHEAVGEIMSLSAATPQHLKS
LDLLEPTFQEDEETEINFLLKQALTIVGTMPFTYMLEKWRWMVFSGEITKQEWTKRWWDM
KREIVGVVEPVPHDETYCDPAALFHVANDYSFIRYYTRTIYQFQFQEALCKAANHTGPLH
KCDITNSTAAGDRLRKLLELGRSKPWTEALENVTGEKYMNAEPLLHYFEPLFEWLKKANS
GRFIGWKTDWAPYSSDAIKVRISLKSALGDQAYEWDESELFLFKSSIAYAMRKYFLDQKK
QEIDFQITDIHVGGETKRISFYLTVSMPGNISDIVPKAVVESAIRMSRGRINEAFRLDDN
TLEFVGIRPTLAPPYEPPVTIWLIVFGVVMGLVVVGVIALVITGQRDRKK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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
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

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