9YGP: HCoV-HKU1 C S 2P

HCoV-HKU1 C S 2P in complex with H501-018 Fab (local cryoEM). Determined by electron microscopy at 3.2 Å resolution. Released 1 Jul 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Human coronavirus HKU1, Homo sapiens
Chains: 4
Atoms: 7,414
Mol. weight: 346.76 kDa
Ligands: NAG
Released: 1 Jul 2026

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

Secondary structure: helices and β-sheets

9YGP contains 28 α-helices and 91 β-strands across 4 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 B: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	34-39	6	1
α-helix	43-45	3
β-strand	49	1	2
β-strand	54-55	2	3
β-strand	60-61	2	4
β-strand	64-68	5	5
α-helix	69	1
β-strand	73-76	4	1
β-strand	80-81	2	6
α-helix	87-90	4
β-strand	96-97	2	7
β-strand	101-107	7	1
β-strand	109-111	3	8
α-helix	113-115	3
β-strand	118-120	3	8
β-strand	123-127	5	7
β-strand	136-139	4	7
β-strand	141	1	7
β-strand	145-151	7	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	183-190	8	7
β-strand	197-205	9	1
β-strand	208-213	6	1
β-strand	220	1	2
β-strand	221-227	7	1
β-strand	234-238	5	7
β-strand	240-241	2	6
β-strand	256-260	5	1
β-strand	261-265	5	5
β-strand	266-267	2	10
β-strand	268-269	2	4
β-strand	270	1	11
β-strand	276	1	11
β-strand	280-281	2	10
α-helix	286-294	9
α-helix	814-818	5
α-helix	823-829	7
α-helix	1041-1045	5
α-helix	1046-1048	3
α-helix	1058-1061	4
α-helix	1067-1086	20

Chain C: 14 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	318-319	2	12
β-strand	326	1	13
α-helix	329-333	5
β-strand	337-338	2	14
α-helix	341-343	3
β-strand	345-349	5	13
β-strand	353-354	2	13
α-helix	356-362	7
β-strand	364-371	8	13
α-helix	375-377	3
β-strand	382-392	11	13
α-helix	393-394	2
α-helix	398-400	3
α-helix	408-412	5
β-strand	422-430	9	13
β-strand	435-436	2	14
α-helix	444-447	4
β-strand	459-463	5	15
β-strand	466-468	3	16
β-strand	477	1	17
α-helix	479-482	4
α-helix	489-491	3
β-strand	492	1	17
α-helix	494-496	3
β-strand	502	1	17
β-strand	504-505	2	18
β-strand	517-518	2	18
β-strand	536-538	3	16
β-strand	550-551	2	19
α-helix	553-555	3
β-strand	556	1	20
β-strand	567	1	20
α-helix	569-571	3
β-strand	572-573	2	19
β-strand	575-579	5	15
β-strand	581-582	2	13
β-strand	585-597	13	13
β-strand	602-604	3	13
α-helix	612-615	4
β-strand	620-624	5	12
β-strand	627-631	5	12
β-strand	632-633	2	21
β-strand	636	1	3
β-strand	647-649	3	3
β-strand	655-659	5	3
β-strand	666-668	3	3
β-strand	669-670	2	21

Chain H: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	18-25	8	22
β-strand	34-39	6	24
β-strand	46-51	6	24
β-strand	57-59	3	24
β-strand	67-72	6	22
β-strand	77-82	6	22
β-strand	89-93	5	24
β-strand	94	1	25
β-strand	101	1	25
β-strand	107-108	2	24
β-strand	110-111	2	23

Chain L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
β-strand	9-13	4	27
β-strand	19-24	6	26
α-helix	27-29	5
β-strand	34-38	5	27
β-strand	45-48	4	27
β-strand	49	1	28
β-strand	53	1	28
β-strand	62-67	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	85-89	5	27
β-strand	90-92	3	29
β-strand	95B-97	3	29
β-strand	102-106	5	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein	B, C	protein	1334	Human coronavirus HKU1	Q0ZME7
H501-018 Fab heavy chain	H	protein	224	Homo sapiens
H501-018 Fab light chain	L	protein	216	Homo sapiens

Sequence of entity 1 (B, C), FASTA

>9YGP_1 Spike glycoprotein (chains B, C)
MFLIIFILPTTLAVIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTT
LLFTGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSE
FSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSE
PLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPL
TCNAISSNTDNETLEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPN
TGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLL
RLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISS
SSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPS
VVNSCAKSKPPSAICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVV
GIGEHCPGLGINEEKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSG
TTCSNDLLYSNTEISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKD
FLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCV
LNAVNLTSYSVSSCDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVE
TVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNIN
SILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSR
SLLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTT
AATVAAMFPPWSAAAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFT
ATNSALAKIQSVVNANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLING
RLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYG
LLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDK
NVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLD
LYYEMNVIQESIKSLNSGRLEVLFQGPGGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH
HHHHSAWSHPQFEK

Sequence of entity 2 (H), FASTA

>9YGP_2 H501-018 Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCSVSGGSISNFYWSWIRQPPGKGLEWIGYIYYTGSSEYN
PSLKSRVILSVDTSKNHFSLKLSSVTAADTAIYYCARGTWSRRLEVDLWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L), FASTA

>9YGP_3 H501-018 Fab light chain (chains L)
QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRSIQRPSGVP
DRFSGSKSGTSASLAISGLRSEDEADYYCATWDDSLNSWVFAGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Primary citation

Human Coronavirus HKU1 Neutralizing Monoclonal Antibodies Target Diverse Epitopes Within and Around the TMPRSS2 Receptor Binding Site. Wang, L., Joseph, J., Vasquez, S. et al. bioRxiv (2025). DOI 10.1101/2025.10.29.685445 · PubMed

Other PDB entries of the same protein (UniProt Q0ZME7), best resolution first:

9YXW 2.6 Å, Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab
8Y8C 2.95 Å, Structure of HCoV-HKU1C spike in the inactive-closed conformation
8Y8B 3.01 Å, Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan
8Y88 3.03 Å, Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
8Y8F 3.07 Å, Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
8Y8A 3.19 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
8Y8G 3.23 Å, Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
8Y87 3.26 Å, Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
8Y89 3.32 Å, Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
9YGN 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 1, global cryoEM)
9YGO 3.4 Å, HuCoV-HKU1 C S 2P in complex with H501-018 Fab (State 2, global cryoEM)
8Y8D 3.41 Å, Structure of HCoV-HKU1C spike in the inactive-1up conformation

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