9BTB: Spike glycoprotein

Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3 sialoglycan (Active state, locally refined). Determined by electron microscopy at 2.33 Å resolution. Released 14 May 2025.

Method: Electron microscopy
Resolution: 2.33 Å
Organism: Human coronavirus HKU1
Chains: 1
Atoms: 2,409
Mol. weight: 153.94 kDa
Ligands: A1AR1, NAG
Released: 14 May 2025

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

Secondary structure: helices and β-sheets

9BTB contains 7 α-helices and 30 β-strands across 1 chain. 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
β-strand	25-26	2	2
α-helix	33	1
β-strand	34-35	2	3
α-helix	36	1
β-strand	46	1	4
β-strand	48	1	4
β-strand	49	1	5
β-strand	59-68	10	6
α-helix	69	1
β-strand	75-76	2	3
β-strand	80-81	2	7
β-strand	85-86	2	2
α-helix	87-90	4
β-strand	96-97	2	8
β-strand	101-107	7	3
β-strand	109-112	4	9
β-strand	117-120	4	9
β-strand	124-127	4	8
β-strand	136-141	6	8
β-strand	145-151	7	8
β-strand	155-160	6	10
β-strand	161-162	2	7
β-strand	173-175	3	10
α-helix	180-182	3
β-strand	183-190	8	8
β-strand	197-205	9	3
β-strand	208-214	7	3
β-strand	220	1	5
β-strand	221-227	7	3
α-helix	231-232	2
β-strand	234-237	4	8
α-helix	238-239	2
β-strand	240-241	2	7
β-strand	256-260	5	3
β-strand	261-270	10	6
β-strand	276-280	5	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	A	protein	1348	Human coronavirus HKU1	Q5MQD0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BTB_1 Spike glycoprotein (chains A)
VIGDFNCTNFAINDLNTTVPRISEYVVDVSYGLGTYYILDRVYLNTTILFTGYFPKSGAN
FRDLSLKGTTYLSTLWYQKPFLSDFNNGIFSRVKNTKLYVNKTLYSEFSTIVIGSVFINN
SYTIVVQPHNGVLEITACQYTMCEYPHTICKSKGSSRNESWHFDKSEPLCLFKKNFTYNV
STDWLYFHFYQERGTFYAYYADSGMPTTFLFSLYLGTLLSHYYVLPLTCNAISSNTDNET
LQYWVTPLSKRQYLLKFDNRGVITNAVDCSSSFFSEIQCKTKSLLPNTGVYDLSGFTVKP
VATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNF
DESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAIN
VTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSA
SCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDE
EKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLLQPN
TEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTNKTYNIFP
CYAGRVSAAFHQNASSLALLYRNLKCSYVLNNISLTTQPYFDSYLGCVFNADNLTDYSVS
SCALRMGSGFCVDYNSPSSSSSRRKRRSISASYRFVTFEPFNVSFVNDSIESVGGLYEIK
IPTNFTIVGQEEFIQTNSPKVTIDCSLFVCSNYAACHDLLSEYGTFCDNINSILDEVNGL
LDTTQLHVADTLMQGVTLSSNLNTNLHFDVDNINFKSLVGCLGPHCGSSSRSFFEDLLFD
KVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSESQISGYTTAATVAAMFP
PWSAAAGIPFSLNVQYRINGLGVTMDVLNKNQKLIATAFNNALLSIQNGFSAPNSALAKI
QSVVNSNAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYV
SQQLSDISLVKFGAALAMEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFMHFSYK
PISFKTVLVSPGLCISGDVGIAPKQGYFIKHNDHWMFTGSSYYYPEPISDKNVVFMNTCS
VNFTKAPLVYLNHSVPKLSDFESELSHWFKNQTSIAPNLTLNLHTINATFLDLYYEMNLI
QESIKSLNNSYINLKDIGTYEMYVKSGGYIPEAPRDGQAYVRKDGEWVLLSTFLNSGRAH
HHHHHGAGGLNDIFEAQKIEWHEDTAAA

Ligands and cofactors

ID	Name	Formula	Copies
A1AR1	5-acetamido-8-O-(5-acetamido-9-O-acetyl-3,5-dideoxy-D-glycero-alpha-D-galacto-n…	C24 H38 N2 O18	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Human coronavirus HKU1 spike structures reveal the basis for sialoglycan specificity and carbohydrate-promoted conformational changes. Jin, M., Hassan, Z., Li, Z. et al. Nat Commun (2025) 16:4158-4158. DOI 10.1038/s41467-025-59137-y · PubMed

Other PDB entries of the same protein (UniProt Q5MQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9JCY 1.8 Å, Crystal structure of the HCoV-HKU1 RBD in complex with Fab
5KWB 1.91 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BT2 1.93 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein D1 (Down State, locally refined)
9BSW 2.06 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDA state)
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
9BT9 2.11 Å, Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined)
9BT1 2.22 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BT0 2.23 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDD state)
5GNB 2.3 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BSX 2.37 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BTA 2.39 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…
9IZN 2.4 Å, Crystal structure of HKU1A RBD bound to TMPRSS2

Browse structure collections

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