9JCX: HCoV-HKU1 RBD and TMPRSS2

Crystal structure of the HCoV-HKU1 RBD and TMPRSS2. Determined by X-ray diffraction at 2.75 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Homo sapiens, Human coronavirus HKU1 (isolate N1)
Chains: 3
Atoms: 5,156
Mol. weight: 78.87 kDa
Ligands: CA, NAG
Released: 30 Jul 2025

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

Secondary structure: helices and β-sheets

9JCX contains 28 α-helices and 63 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	118-119	2	1
β-strand	126-127	2	1
α-helix	129-131	3
β-strand	149-152	4	2
β-strand	157-162	6	2
β-strand	167-170	4	2
β-strand	171	1	3
β-strand	172	1	2
α-helix	178-187	10
β-strand	196-200	5	2
β-strand	209-212	4	3
α-helix	214-216	3
α-helix	221-223	3
β-strand	225-228	4	3
β-strand	236-240	5	2

Chain B: 15 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	326	1	10
α-helix	329-333	5
β-strand	337-339	3	11
α-helix	340	1
β-strand	345-349	5	12
β-strand	352-354	3	10
α-helix	356-362	7
β-strand	367-371	5	12
α-helix	375-377	3
β-strand	382-383	2	10
β-strand	385-392	8	12
α-helix	395-401	7
α-helix	408-412	5
β-strand	415	1	13
β-strand	422-430	9	12
α-helix	431-433	3
β-strand	435-437	3	11
α-helix	443-447	5
β-strand	459-463	5	14
β-strand	467-468	2	15
β-strand	477	1	16
α-helix	478	1
α-helix	479-483	5
β-strand	487	1	17
α-helix	489-491	3
β-strand	492	1	16
β-strand	494	1	18
α-helix	495-496	2
α-helix	500-502	3
β-strand	504-509	6	17
β-strand	512-518	7	17
β-strand	536-537	2	15
β-strand	542	1	13
β-strand	551	1	19
α-helix	553-555	3
β-strand	556	1	20
β-strand	558	1	16
β-strand	566	1	18
β-strand	569	1	20
α-helix	571-573	3
β-strand	574	1	19
β-strand	577-581	5	14
β-strand	583-584	2	12
β-strand	587-597	11	12
β-strand	604-606	3	10

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	257	1	4
β-strand	260-261	2	5
α-helix	262-263	2
β-strand	270-275	6	6
β-strand	278-287	10	6
β-strand	290-293	4	6
α-helix	296-298	3
α-helix	305-307	3
β-strand	308-312	5	6
β-strand	316	1	7
α-helix	317-319	3
β-strand	326-333	8	6
β-strand	338	1	8
β-strand	343	1	8
β-strand	347-351	5	6
α-helix	363-364	2
β-strand	365	1	5
α-helix	366-368	3
β-strand	378-383	6	5
α-helix	392-394	3
β-strand	396	1	7
β-strand	398-405	8	5
α-helix	407-410	4
β-strand	424-428	5	5
β-strand	435	1	4
β-strand	444-449	6	5
β-strand	452-461	10	5
β-strand	467	1	9
β-strand	470	1	9
β-strand	472-476	5	5
α-helix	481-492	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2 non-catalytic chain	A	protein	146	Homo sapiens	O15393 (AlphaFold model)
Transmembrane protease serine 2 catalytic chain	C	protein	249	Homo sapiens	O15393 (AlphaFold model)
Spike protein S1	B	protein	308	Human coronavirus HKU1 (isolate N1)	Q5MQD0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9JCX_1 Transmembrane protease serine 2 non-catalytic chain (chains A)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDK

Sequence of entity 2 (C), FASTA

>9JCX_2 Transmembrane protease serine 2 catalytic chain (chains C)
IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGIL
RQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQP
EQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVD
SCQGDAGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFV
EHHHHHHHH

Sequence of entity 3 (B), FASTA

>9JCX_3 Spike protein S1 (chains B)
DLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSC
FKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPS
SWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYR
SCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGS
YNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCSNDLSGLEVLFQGPGGS
HHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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 O15393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V04 1.58 Å, High resolution TMPRSS2 structure following acylation by nafamostat
8S0L 1.8 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
9JD1 1.9 Å, Crystal structure of TMPRSS2 in complex with Fab
7MEQ 1.95 Å, Crystal structure of human TMPRSS2 in complex with Nafamostat
9JD0 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody
9U8G 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody77_10
9E83 2.07 Å, TMPRSS2 crystal structure following acylation by UCSF_157
8V1F 2.19 Å, TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
8S0N 2.3 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
7Y0E 2.39 Å, Crystal structure of TMPRSS2 in complex with Camostat
8HD8 2.4 Å, Crystal structure of TMPRSS2 in complex with 212-148
9IZN 2.4 Å, Crystal structure of HKU1A RBD bound to TMPRSS2

Browse structure collections

About this viewer

MolViewer shows 9JCX directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.