9JCY: HCoV-HKU1 RBD

Crystal structure of the HCoV-HKU1 RBD in complex with Fab. Determined by X-ray diffraction at 1.8 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Human coronavirus HKU1 (isolate N1), Homo sapiens
Chains: 3
Atoms: 6,231
Mol. weight: 83.33 kDa
Ligands: NAG
Released: 30 Jul 2025

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

Secondary structure: helices and β-sheets

9JCY contains 33 α-helices and 72 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: 17 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	324-325	2
β-strand	326	1	1
α-helix	329-333	5
β-strand	337-339	3	2
α-helix	341-343	3
β-strand	345-349	5	3
β-strand	352-354	3	1
α-helix	356-362	7
β-strand	364-371	8	3
α-helix	375-377	3
β-strand	382-383	2	1
β-strand	385-392	8	3
α-helix	395-401	7
α-helix	408-412	5
β-strand	422-430	9	3
β-strand	435-437	3	2
α-helix	443-447	5
α-helix	450-453	4
β-strand	459-463	5	4
β-strand	467-468	2	5
β-strand	477	1	6
α-helix	478	1
α-helix	479-482	4
β-strand	487	1	7
α-helix	489-491	3
β-strand	492	1	6
β-strand	494	1	8
α-helix	495-496	2
α-helix	501-503	3
β-strand	504-509	6	7
β-strand	512-518	7	7
β-strand	536-537	2	5
α-helix	544-546	3
β-strand	551	1	9
α-helix	553-555	3
β-strand	556	1	10
β-strand	558	1	6
β-strand	566	1	8
β-strand	569	1	10
α-helix	571-573	3
β-strand	574	1	9
β-strand	577-581	5	4
β-strand	583-584	2	3
β-strand	587-597	11	3
β-strand	604-606	3	1

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	18
α-helix	112-113	2
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	191-197	7	20
β-strand	205-210	6	20

Chain C: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	11
β-strand	18-25	8	7
β-strand	34-40	7	12
β-strand	47-52	6	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	12
β-strand	109-112	4	12
β-strand	118-120	3	12
β-strand	121-122	2	11
α-helix	126-127	2
β-strand	128	1	13
α-helix	129-130	2
β-strand	131-135	5	14
α-helix	136-138	3
β-strand	146-156	11	14
β-strand	157	1	13
β-strand	162-165	4	15
α-helix	166-168	3
β-strand	170	1	15
β-strand	174-176	3	14
α-helix	177-179	3
β-strand	180-181	2	14
β-strand	187-196	10	14
α-helix	197-199	3
β-strand	206-211	6	15
α-helix	212-214	3
β-strand	216-221	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	308	Human coronavirus HKU1 (isolate N1)	Q5MQD0 (AlphaFold model)
Heavy chain of Fab	C	protein	235	Homo sapiens
Light chain of Fab	B	protein	214	Homo sapiens

Sequence of entity 1 (A), FASTA

>9JCY_1 Spike protein S1 (chains A)
DLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSC
FKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPS
SWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYR
SCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGS
YNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLSGLEVLFQGPGGS
HHHHHHHH

Sequence of entity 2 (C), FASTA

>9JCY_2 Heavy chain of Fab (chains C)
QVQLQESGPGLVKPSGTLSLTCAVSGGSISSSNWWSWVRQPPGKGLEWIGSMHYSGSSHY
KPSLKSRIAMSVDTSKNQFSLNLNSVTAADTAVYYCAREGGSSGYDYVYYFDDWGQGTTV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 3 (B), FASTA

>9JCY_3 Light chain of Fab (chains B)
DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPRTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Water and common crystallization additives (GOL) are not listed.

Primary citation

The crystal structure of coronavirus RBD-TMPRSS2 complex provides basis for the discovery of therapeutic antibodies. Zhao, Z., Yang, Q., Liu, X. et al. Nat Commun (2025) 16:6636-6636. DOI 10.1038/s41467-025-62023-2 · PubMed

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

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…
9BTB 2.33 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…
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

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