9YXW: HCoV-HKU1 RBD bound by H501-008 Fab

Crystal structure of HCoV-HKU1 RBD bound by H501-008 Fab. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Jul 2026.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Human coronavirus HKU1, Homo sapiens
Chains: 3
Atoms: 5,659
Mol. weight: 82.93 kDa
Released: 1 Jul 2026

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

Secondary structure: helices and β-sheets

9YXW contains 31 α-helices and 78 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.

Chain A: 16 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	329-333	5
β-strand	337-339	3	1
α-helix	341-343	3
β-strand	345-350	6	2
β-strand	354	1	3
α-helix	356-362	7
β-strand	364-371	8	2
α-helix	375-377	3
β-strand	382-383	2	4
β-strand	385-392	8	2
α-helix	393-394	2
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	5
β-strand	422-430	9	2
β-strand	435-437	3	1
α-helix	443-447	5
β-strand	459-463	5	6
β-strand	466-468	3	7
β-strand	473-477	5	8
α-helix	478	1
α-helix	479-482	4
β-strand	487	1	9
β-strand	492	1	8
β-strand	494	1	10
α-helix	495-496	2
β-strand	500-502	3	8
α-helix	503	1
β-strand	504-507	4	9
β-strand	515-518	4	9
β-strand	536-538	3	7
β-strand	542	1	5
α-helix	544-546	3
β-strand	550-551	2	11
α-helix	553-555	3
β-strand	556	1	12
β-strand	558	1	8
β-strand	564	1	10
α-helix	565	1
β-strand	567	1	12
α-helix	569-571	3
β-strand	572-573	2	11
β-strand	575-579	5	6
β-strand	581-582	2	2
β-strand	585-595	11	2
β-strand	602-603	2	4
β-strand	604	1	3

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	57-59	3	15
β-strand	65-70	6	13
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	89-95	7	15
β-strand	100N-103	4	15
β-strand	107-108	2	15
β-strand	109-111	3	14
β-strand	117	1	16
α-helix	118-119	2
β-strand	120-124	5	17
α-helix	125-127	3
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
α-helix	186-188	3
β-strand	194-200	7	18
α-helix	201-203	3
β-strand	205-211	7	18

Chain L: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
β-strand	5	1	20
β-strand	9-13	4	21
β-strand	19-24	6	20
α-helix	27-29	5
β-strand	34-38	5	21
α-helix	43-44	2
β-strand	45-48	4	21
β-strand	49	1	22
β-strand	53	1	22
β-strand	62-67	6	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	84-92	9	21
β-strand	95B-98	4	21
β-strand	99	1	19
β-strand	102-106	5	21
β-strand	112	1	23
α-helix	113-114	2
β-strand	115-119	5	24
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	24
β-strand	141	1	23
β-strand	146-151	6	25
β-strand	154-156	3	25
β-strand	160-162	3	24
α-helix	163-165	3
β-strand	166-167	2	24
β-strand	173-181	9	24
α-helix	183-188	6
β-strand	192-198	7	25
β-strand	201-207	7	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	305	Human coronavirus HKU1	Q0ZME7
H501-008 Fab heavy chain	H	protein	243	Homo sapiens
H501-008 Fab light chain	L	protein	216	Homo sapiens

Sequence of entity 1 (A), FASTA

>9YXW_1 Spike protein S1 (chains A)
TVKPVATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFS
CNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSL
PLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSK
PPSAICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGL
GINEEKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDGSL
EVLFQ

Sequence of entity 2 (H), FASTA

>9YXW_2 H501-008 Fab heavy chain (chains H)
QVQLVQSGGGVVQPGRSLRLSCAVSGFTLDRYAMHWVRQAPGKALEWVALMSADGREQYY
AESVKGRFTFSRDSSKNTLYLQMHNLRTDDSSVYFCAREGPMYYDAWSGRSYYNNYALDV
WGRGTTVAVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEV
LFQ

Sequence of entity 3 (L), FASTA

>9YXW_3 H501-008 Fab light chain (chains L)
QSVLTQPPSVSAAPGQTVTISCSGSSSNIGDNYVSWYQQVPGTAPRLLVYDNNRRPLGIP
DRFSGSKSGTSATLAIAGLQTGDEADYYCGTWDSSLSAGVFGGGTKLTVVGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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:

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
9YGP 3.2 Å, HCoV-HKU1 C S 2P in complex with H501-018 Fab (local cryoEM)
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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