9JD0: TMPRSS2
Crystal structure of TMPRSS2 in complex with nanobody. Determined by X-ray diffraction at 2.0 Å resolution. Released 30 Jul 2025.
- Method
- X-ray diffraction
- Resolution
- 2.0 Å
- Organisms
- Homo sapiens, Vicugna pacos
- Chains
- 6
- Atoms
- 8,455
- Mol. weight
- 118.25 kDa
- Ligands
- CA, NAG, MLI
- Released
- 30 Jul 2025
Explore 9JD0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9JD0 contains 35 α-helices and 84 β-strands across 6 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: 3 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 | 221-223 | 3 | |
| β-strand | 225-228 | 4 | 3 |
| β-strand | 236-240 | 5 | 2 |
Chain B: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 118-119 | 2 | 4 |
| β-strand | 126-127 | 2 | 4 |
| α-helix | 129-131 | 3 | |
| α-helix | 143-145 | 3 | |
| β-strand | 149-152 | 4 | 5 |
| β-strand | 157-162 | 6 | 5 |
| β-strand | 167-170 | 4 | 5 |
| β-strand | 171 | 1 | 6 |
| β-strand | 172 | 1 | 5 |
| α-helix | 178-188 | 11 | |
| β-strand | 196-200 | 5 | 5 |
| β-strand | 209-212 | 4 | 6 |
| α-helix | 221-223 | 3 | |
| β-strand | 225-228 | 4 | 6 |
| β-strand | 236-240 | 5 | 5 |
Chain C: 9 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 257 | 1 | 7 |
| β-strand | 260-261 | 2 | 8 |
| α-helix | 262-263 | 2 | |
| β-strand | 270-275 | 6 | 9 |
| β-strand | 278-285 | 8 | 9 |
| β-strand | 290-293 | 4 | 9 |
| α-helix | 295-297 | 3 | |
| α-helix | 305-307 | 3 | |
| β-strand | 308-312 | 5 | 9 |
| β-strand | 316 | 1 | 10 |
| α-helix | 317-319 | 3 | |
| β-strand | 326-333 | 8 | 9 |
| β-strand | 338 | 1 | 11 |
| β-strand | 343 | 1 | 11 |
| β-strand | 347-351 | 5 | 9 |
| α-helix | 363-364 | 2 | |
| β-strand | 365 | 1 | 8 |
| α-helix | 366-368 | 3 | |
| β-strand | 378-383 | 6 | 8 |
| α-helix | 391-394 | 4 | |
| β-strand | 396 | 1 | 10 |
| β-strand | 398-405 | 8 | 8 |
| α-helix | 407-410 | 4 | |
| β-strand | 424-428 | 5 | 8 |
| β-strand | 435 | 1 | 7 |
| β-strand | 444-449 | 6 | 8 |
| β-strand | 452-461 | 10 | 8 |
| β-strand | 467 | 1 | 12 |
| β-strand | 470 | 1 | 12 |
| β-strand | 472-476 | 5 | 8 |
| α-helix | 477-492 | 16 | |
Chain D: 10 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 257 | 1 | 13 |
| β-strand | 260-261 | 2 | 14 |
| α-helix | 262-263 | 2 | |
| β-strand | 270-275 | 6 | 15 |
| β-strand | 278-285 | 8 | 15 |
| β-strand | 290-293 | 4 | 15 |
| α-helix | 295-297 | 3 | |
| α-helix | 305-307 | 3 | |
| β-strand | 308-312 | 5 | 15 |
| β-strand | 316 | 1 | 16 |
| α-helix | 317-319 | 3 | |
| β-strand | 326-333 | 8 | 15 |
| β-strand | 338 | 1 | 17 |
| β-strand | 343 | 1 | 17 |
| β-strand | 347-351 | 5 | 15 |
| α-helix | 354-357 | 4 | |
| α-helix | 363-364 | 2 | |
| β-strand | 365 | 1 | 14 |
| α-helix | 366-368 | 3 | |
| β-strand | 378-383 | 6 | 14 |
| α-helix | 391-394 | 4 | |
| β-strand | 396 | 1 | 16 |
| β-strand | 398-405 | 8 | 14 |
| α-helix | 407-410 | 4 | |
| β-strand | 424-428 | 5 | 14 |
| β-strand | 435 | 1 | 13 |
| β-strand | 444-449 | 6 | 14 |
| β-strand | 452-461 | 10 | 14 |
| β-strand | 472-476 | 5 | 14 |
| α-helix | 477-491 | 15 | |
Chain E: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 20 |
| β-strand | 10-12 | 3 | 21 |
| β-strand | 18-25 | 8 | 20 |
| α-helix | 28-31 | 4 | |
| β-strand | 33-39 | 7 | 21 |
| β-strand | 46-52 | 7 | 21 |
| β-strand | 58-60 | 3 | 21 |
| β-strand | 68-73 | 6 | 20 |
| β-strand | 78-83 | 6 | 20 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-97 | 6 | 21 |
| α-helix | 99-102 | 4 | |
| α-helix | 110-112 | 3 | |
| α-helix | 113-115 | 3 | |
| β-strand | 116-121 | 6 | 21 |
Chain F: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 18 |
| β-strand | 10-11 | 2 | 19 |
| β-strand | 18-25 | 8 | 18 |
| α-helix | 28-30 | 3 | |
| β-strand | 33-39 | 7 | 19 |
| β-strand | 46-52 | 7 | 19 |
| β-strand | 58-60 | 3 | 19 |
| β-strand | 68-73 | 6 | 18 |
| β-strand | 78-83 | 6 | 18 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-97 | 6 | 19 |
| α-helix | 99-102 | 4 | |
| α-helix | 110-112 | 3 | |
| β-strand | 116-120 | 5 | 19 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transmembrane protease serine 2 non-catalytic chain | A, B | protein | 146 | Homo sapiens | O15393 (AlphaFold model) |
| Transmembrane protease serine 2 catalytic chain | C, D | protein | 249 | Homo sapiens | O15393 (AlphaFold model) |
| Nanobody | E, F | protein | 131 | Vicugna pacos | |
Sequence of entity 1 (A, B), FASTA
>9JD0_1 Transmembrane protease serine 2 non-catalytic chain (chains A, B)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDK
Sequence of entity 2 (C, D), FASTA
>9JD0_2 Transmembrane protease serine 2 catalytic chain (chains C, D)
IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGIL
RQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQP
EQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVD
SCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFV
EHHHHHHHH
Sequence of entity 3 (E, F), FASTA
>9JD0_3 Nanobody (chains E, F)
AVQLQASGGGFVQPGGSLRLSCAASGKVVEQGLMGWFRQAPGKEREFVSAIQYDTKLEYY
ADSVKGRFTISRDNSKNTVYLQMNSLRAEDTATYYCATPQMWVQRDVQARWYWGQGTQVT
VSSGSHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 2 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| MLI | Malonate ion | C3 H2 O4 | 4 |
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 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
- 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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