9KR9: Spike glycoprotein

Overall structure of HKU5 S protein with S468A/Y463A mutation. Determined by electron microscopy at 2.8 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Bat coronavirus HKU5
Chains: 3
Atoms: 28,851
Mol. weight: 468.59 kDa
Ligands: NAG, PLM
Released: 5 Nov 2025

Explore 9KR9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KR9 contains 132 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: 44 helices, 80 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-39	3	1
α-helix	63	1
β-strand	64	1	2
α-helix	65-66	2
β-strand	74-82	9	3
α-helix	83-84	2
β-strand	90-92	3	4
β-strand	95-96	2	5
β-strand	99-100	2	6
β-strand	103-104	2	6
β-strand	107-109	3	1
β-strand	117-118	2	7
β-strand	122-127	6	4
β-strand	134-137	4	8
β-strand	140-146	7	8
β-strand	147-148	2	9
β-strand	154-157	4	7
β-strand	160-163	4	10
β-strand	168-172	5	10
β-strand	175-182	8	7
β-strand	187-197	11	7
β-strand	214	1	11
α-helix	218-221	4
α-helix	231-239	9
β-strand	240-243	4	7
β-strand	248-252	5	7
β-strand	260-267	8	4
β-strand	270-275	6	4
β-strand	286	1	2
β-strand	287-292	6	4
α-helix	297-298	2
β-strand	300-303	4	7
α-helix	304-305	2
β-strand	306	1	11
β-strand	307-308	2	5
α-helix	312-314	3
β-strand	317-318	2	9
β-strand	321-325	5	4
β-strand	327-335	9	3
β-strand	341-346	6	3
α-helix	351-359	9
β-strand	367-370	4	12
β-strand	380-384	5	13
β-strand	389-390	2	14
α-helix	391	1
α-helix	394-396	3
β-strand	399	1	15
α-helix	400-403	4
α-helix	404-406	3
β-strand	408-412	5	16
β-strand	415-417	3	14
α-helix	419-423	5
β-strand	427-434	8	16
α-helix	440-442	3
β-strand	446	1	17
β-strand	448-455	8	16
α-helix	461-463	3
α-helix	471-475	5
β-strand	485-492	8	16
β-strand	499	1	15
β-strand	504-514	11	18
β-strand	519-521	3	18
α-helix	523-525	3
β-strand	545-548	4	18
β-strand	552-560	9	18
β-strand	565-574	10	16
β-strand	582	1	17
β-strand	583-584	2	14
β-strand	601-606	6	13
β-strand	609-618	10	13
β-strand	628-630	3	13
β-strand	636-640	5	13
β-strand	646-650	5	13
β-strand	658-662	5	12
β-strand	667-673	7	12
α-helix	689-697	9
β-strand	704-705	2	12
β-strand	709-712	4	12
β-strand	716-721	6	19
β-strand	727	1	19
β-strand	732-735	4	19
β-strand	755-759	5	19
α-helix	764-766	3
α-helix	768-770	3
β-strand	775-793	19	20
β-strand	799-801	3	21
α-helix	803-807	5
α-helix	812-817	6
α-helix	818-821	4
α-helix	824-846	23
α-helix	847-849	3
β-strand	855	1	22
α-helix	857-859	3
β-strand	862-863	2	23
β-strand	866-867	2	23
α-helix	873-875	3
α-helix	886-892	7
α-helix	905-911	7
α-helix	924-927	4
β-strand	929-931	3	21
α-helix	932-934	3
α-helix	941-949	9
β-strand	951	1	22
β-strand	964-965	2	24
α-helix	969-977	9
α-helix	984-989	6
α-helix	991-1002	12
α-helix	1005-1007	3
α-helix	1017-1034	18
α-helix	1035-1037	3
α-helix	1048-1054	7
α-helix	1057-1099	43
α-helix	1100-1104	5
β-strand	1118-1127	10	20
β-strand	1130-1149	20	20
β-strand	1152-1153	2	25
β-strand	1161-1164	4	25
β-strand	1167-1171	5	20
β-strand	1185-1189	5	20
β-strand	1192-1196	5	20
β-strand	1203-1205	3	25
β-strand	1213-1214	2	25
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

>9KR9_1 Spike glycoprotein (chains A, B, C)
MIRSVLVLMCSLTFIGNLTRGQSVDMGHNGTGSCLDSQVQPDYFESVHTTWPMPIDTSKA
EGVIYPNGKSYSNITLTYTGLYPKANDLGKQYLFSDGHSAPGRLNNLFVSNYSSQVESFD
DGFVVRIGAAANKTGTTVISQSTFKPIKKIYPAFLLGHSVGNYTPSNRTGRYLNHTLVIL
PDGCGTILHAFYCVLHPRTQQNCAGETNFKSLSLWDTPASDCVSGSYNQEATLGAFKVYF
DLINCTFRYNYTITEDENAEWFGITQDTQGVHLYSSRKENVFRNNMFHFATLPVYQKILY
YTVIPRSIRSPFNDRKAWAAFYIYKLHPLTYLLNFDVEGYITKAVDCGYDDLAQLQCSYE
SFEVETGVYSVSSFEASPRGEFIEQATTQECDFTPMLTGTPPPIYNFKRLVFTNCNYNLT
KLLSLFQVSEFSCHQVSPSSLATGCYSSLTVDYFAYSTDMSSALQPGAAGAIVQFNYKQD
FSNPTCRVLATVPQNLTTITKPSNYAYLTECYKTSAYGKNYLYNAPGAYTPCLSLASRGF
STKYQSHSDGELTTTGYIYPVTGNLQMAFIISVQYGTDTNSVCPMQALRNDTSIEDKLDV
CVEYSLHGITGRGVFHNCTSVGLRNQRFVYDTFDNLVGYHSDNGNYYCVRPCVSVPVSVI
YDKASNSHATLFGSVACSHVTTMMSQFSRMTKTNLLARTTPGPLQTTVGCAMGFINSSMV
VDECQLPLGQSLCAIPPTTSSRVRRATSGASDVFQIATLNFTSPLTLAPINSTGFVVAVP
TNFTFGVTQEFIETTIQKITVDCKQYVCNGFKKCEDLLKEYGQFCSKINQALHGANLRQD
ESIANLFSSIKTQNTQPLQAGLNGDFNLTMLQIPQVTTGERKYRSTIEDLLFNKVTIADP
GYMQGYDECMQQGPQSARDLICAQYVAGYKVLPPLYDPYMEAAYTSSLLGSIAGASWTAG
LSSFAAIPFAQSIFYRLNGVGITQQVLSENQKIIANKFNQALGAMQTGFTTTNLAFNKVQ
DAVNANAMALSKLAAELSNTFGAISSSISDILARLDTVEQEAQIDRLINGRLTSLNAFVA
QQLVRTEAAARSAQLAQDKVNECVKSQSKRNGFCGTGTHIVSFAINAPNGLYFFHVGYQP
TSHVNATAAYGLCNTENPQKCIAPIDGYFVLNQTTSTVADSDQQWYYTGSSFFHPEPITE
ANSKYVSMDVKFENLTNRLPPPLLSNSTDLDFKEELEEFFKNVSSQGPNFQEISKINTTL
LNLNTELMVLSEVVKQLNESYIDLKELGNYTFYQKWPWYIWLGFIAGLVALALCVFFILC
CTGCGTSCLGKLKCNRCCDSYDEYEVEKIHVH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	30
PLM	Palmitic acid	C16 H32 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…
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
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

Browse structure collections

About this viewer

MolViewer shows 9KR9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.