9JD1: TMPRSS2

Crystal structure of TMPRSS2 in complex with Fab. Determined by X-ray diffraction at 1.9 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,955
Mol. weight: 94.74 kDa
Ligands: CA
Released: 30 Jul 2025

Explore 9JD1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JD1 contains 31 α-helices and 79 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 A: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	6
β-strand	9-12	4	7
β-strand	18-24	7	6
α-helix	29-31	3
β-strand	35-39	5	7
β-strand	46-49	4	7
β-strand	50	1	8
β-strand	54	1	8
β-strand	63-68	6	6
β-strand	73-78	6	6
α-helix	83-85	3
β-strand	87-94	8	7
β-strand	99-101	3	7
β-strand	102	1	6
β-strand	105-109	5	7
β-strand	114	1	9
α-helix	115-116	2
β-strand	117-121	5	10
α-helix	122-124	3
α-helix	125-128	4
β-strand	132-142	11	10
β-strand	143	1	9
β-strand	148-153	6	11
β-strand	156-157	2	11
α-helix	158	1
β-strand	162-166	5	10
α-helix	167-170	4
β-strand	176-185	10	10
α-helix	186-189	4
β-strand	194-200	7	11
β-strand	208-213	6	11

Chain B: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	12
α-helix	74-76	3
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	101-105	5	15
β-strand	110-115	6	15
β-strand	118-119	2	14
β-strand	123-125	3	14
β-strand	126-127	2	13
α-helix	131-132	2
β-strand	133	1	16
α-helix	134-135	2
β-strand	136-140	5	17
α-helix	141-143	3
β-strand	151-161	11	17
β-strand	162	1	16
β-strand	167-170	4	18
α-helix	171-173	3
β-strand	175	1	18
β-strand	179-181	3	17
α-helix	182-184	3
β-strand	185-186	2	17
β-strand	192-201	10	17
α-helix	202-204	3
β-strand	210-216	7	18
α-helix	217-219	3
β-strand	221-227	7	18

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	119	1	19
β-strand	126	1	19
α-helix	129-131	3
α-helix	143-145	3
β-strand	149-152	4	20
β-strand	157-162	6	20
β-strand	167-170	4	20
β-strand	171	1	21
β-strand	172	1	20
α-helix	178-188	11
β-strand	196-200	5	20
β-strand	209-212	4	21
α-helix	221-224	4
β-strand	225-228	4	21
β-strand	236-240	5	20

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	257	1	1
β-strand	260-261	2	2
α-helix	262-263	2
β-strand	270-275	6	3
β-strand	278-285	8	3
β-strand	290-293	4	3
α-helix	295-298	4
α-helix	305-307	3
β-strand	308-312	5	3
β-strand	316	1	4
α-helix	317-319	3
β-strand	326-333	8	3
β-strand	338	1	5
β-strand	343	1	5
β-strand	347-351	5	3
α-helix	363-364	2
β-strand	365	1	2
α-helix	366-368	3
β-strand	378-383	6	2
α-helix	392-394	3
β-strand	396	1	4
β-strand	398-405	8	2
α-helix	407-410	4
β-strand	424-428	5	2
β-strand	435	1	1
β-strand	444-449	6	2
β-strand	452-461	10	2
β-strand	472-476	5	2
α-helix	477-492	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2 catalytic chain	D	protein	249	Homo sapiens	O15393 (AlphaFold model)
Light chain of Fab	A	protein	217	Homo sapiens
Heavy chain of Fab	B	protein	240	Homo sapiens
Transmembrane protease serine 2 non-catalytic chain	C	protein	146	Homo sapiens	O15393 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>9JD1_1 Transmembrane protease serine 2 catalytic chain (chains D)
IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGIL
RQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQP
EQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVD
SCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFV
EHHHHHHHH

Sequence of entity 2 (A), FASTA

>9JD1_2 Light chain of Fab (chains A)
NFMLTQPHSMSESPGKTVTISCTRSSGSIASNYVQWYQQRPGSSPTTVIYDDNQRPSGVP
DRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNVIFGGGTKLTVLRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B), FASTA

>9JD1_3 Heavy chain of Fab (chains B)
QVQLQESGGDLVQPGGSLRLSCAASGFTFSSSAMTWVRQAPGKGLEWVSDISRNGGSTNY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAREGYDFWSGRERRYYYYGMDVWG
QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 4 (C), FASTA

>9JD1_4 Transmembrane protease serine 2 non-catalytic chain (chains C)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (MES, 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 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
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
7XYD 2.58 Å, Crystal structure of TMPRSS2 in complex with Nafamostat

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