Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined). Determined by electron microscopy at 2.11 Å resolution. Released 14 May 2025.
Explore 9BT9 in 3D Show helices and sheets RCSB PDB PDBe
9BT9 contains 5 α-helices and 28 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 18 | 1 | 1 |
| β-strand | 25-26 | 2 | 2 |
| β-strand | 34-39 | 6 | 3 |
| β-strand | 49 | 1 | 4 |
| β-strand | 59-68 | 10 | 5 |
| α-helix | 69 | 1 | |
| β-strand | 73-76 | 4 | 3 |
| β-strand | 80-81 | 2 | 6 |
| β-strand | 85-86 | 2 | 2 |
| α-helix | 87-90 | 4 | |
| β-strand | 96-97 | 2 | 7 |
| β-strand | 101-107 | 7 | 3 |
| β-strand | 109-113 | 5 | 8 |
| β-strand | 116-120 | 5 | 8 |
| β-strand | 124-127 | 4 | 7 |
| β-strand | 137-142 | 6 | 7 |
| β-strand | 145-150 | 6 | 7 |
| β-strand | 155-160 | 6 | 9 |
| β-strand | 161-162 | 2 | 6 |
| β-strand | 173-175 | 3 | 9 |
| α-helix | 180-182 | 3 | |
| β-strand | 185-190 | 6 | 7 |
| β-strand | 197-205 | 9 | 3 |
| β-strand | 208-214 | 7 | 3 |
| β-strand | 220 | 1 | 4 |
| β-strand | 221-227 | 7 | 3 |
| α-helix | 231-232 | 2 | |
| β-strand | 234-237 | 4 | 7 |
| α-helix | 238-239 | 2 | |
| β-strand | 240-241 | 2 | 6 |
| β-strand | 256-260 | 5 | 3 |
| β-strand | 261-270 | 10 | 5 |
| β-strand | 276-280 | 5 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Spike glycoprotein | A | protein | 1348 | Human coronavirus HKU1 | Q5MQD0 (AlphaFold model) |
>9BT9_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
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 4 |
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:
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