7L2T: DkTx-bound minimal TRPV1 in partial open state
cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state. Determined by electron microscopy at 3.08 Å resolution. Released 22 Sept 2021.
- Method
- Electron microscopy
- Resolution
- 3.08 Å
- Organisms
- Rattus norvegicus, Cyriopagopus schmidti
- Chains
- 6
- Atoms
- 20,167
- Mol. weight
- 313.79 kDa
- Ligands
- 65I, XJ7
- Released
- 22 Sept 2021
Explore 7L2T in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7L2T contains 134 α-helices and 58 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: 32 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 157-163 | 7 | |
| β-strand | 166 | 1 | 1 |
| β-strand | 169 | 1 | 1 |
| α-helix | 172-183 | 12 | |
| α-helix | 187-190 | 4 | |
| β-strand | 193 | 1 | 2 |
| β-strand | 203 | 1 | 2 |
| α-helix | 204-210 | 7 | |
| α-helix | 214-222 | 9 | |
| α-helix | 234-236 | 3 | |
| α-helix | 251-257 | 7 | |
| α-helix | 261-268 | 8 | |
| α-helix | 287-293 | 7 | |
| α-helix | 299-319 | 21 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-352 | 7 | |
| α-helix | 363-365 | 3 | |
| β-strand | 368-373 | 6 | 3 |
| β-strand | 377-383 | 7 | 3 |
| α-helix | 395-400 | 6 | |
| α-helix | 411-414 | 4 | |
| α-helix | 416-425 | 10 | |
| α-helix | 426-430 | 5 | |
| α-helix | 431-453 | 23 | |
| α-helix | 464-466 | 3 | |
| α-helix | 469-499 | 31 | |
| α-helix | 505-508 | 4 | |
| α-helix | 511-531 | 21 | |
| α-helix | 537-550 | 14 | |
| α-helix | 551-556 | 6 | |
| α-helix | 560-572 | 13 | |
| α-helix | 573-577 | 5 | |
| α-helix | 578-598 | 21 | |
| α-helix | 630-641 | 12 | |
| α-helix | 659-681 | 23 | |
| α-helix | 682-684 | 3 | |
| α-helix | 689-711 | 23 | |
| β-strand | 726 | 1 | 4 |
| β-strand | 738 | 1 | 4 |
| β-strand | 741-747 | 7 | 3 |
Chain B: 30 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 157-163 | 7 | |
| β-strand | 166 | 1 | 17 |
| β-strand | 169 | 1 | 17 |
| α-helix | 171-183 | 13 | |
| α-helix | 187-190 | 4 | |
| β-strand | 193 | 1 | 18 |
| β-strand | 203 | 1 | 18 |
| α-helix | 204-210 | 7 | |
| α-helix | 214-222 | 9 | |
| α-helix | 234-236 | 3 | |
| α-helix | 251-257 | 7 | |
| α-helix | 261-268 | 8 | |
| α-helix | 287-293 | 7 | |
| α-helix | 299-319 | 21 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-353 | 8 | |
| α-helix | 363-365 | 3 | |
| β-strand | 368-373 | 6 | 19 |
| β-strand | 377-382 | 6 | 19 |
| α-helix | 395-400 | 6 | |
| α-helix | 416-425 | 10 | |
| α-helix | 426-430 | 5 | |
| α-helix | 431-453 | 23 | |
| α-helix | 463-466 | 4 | |
| α-helix | 469-499 | 31 | |
| α-helix | 505-508 | 4 | |
| α-helix | 511-531 | 21 | |
| α-helix | 537-550 | 14 | |
| α-helix | 551-556 | 6 | |
| α-helix | 560-572 | 13 | |
| α-helix | 573-577 | 5 | |
| α-helix | 578-598 | 21 | |
| α-helix | 630-641 | 12 | |
| α-helix | 659-680 | 22 | |
| α-helix | 689-711 | 23 | |
| β-strand | 726 | 1 | 20 |
| β-strand | 738 | 1 | 20 |
| β-strand | 742-747 | 6 | 19 |
Chain C: 31 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 157-163 | 7 | |
| β-strand | 166 | 1 | 21 |
| β-strand | 169 | 1 | 21 |
| α-helix | 172-183 | 12 | |
| α-helix | 187-190 | 4 | |
| β-strand | 193 | 1 | 22 |
| β-strand | 203 | 1 | 22 |
| α-helix | 204-210 | 7 | |
| α-helix | 214-222 | 9 | |
| α-helix | 234-236 | 3 | |
| α-helix | 251-257 | 7 | |
| α-helix | 261-268 | 8 | |
| α-helix | 287-293 | 7 | |
| α-helix | 299-319 | 21 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-352 | 7 | |
| α-helix | 363-365 | 3 | |
| β-strand | 368-373 | 6 | 23 |
| β-strand | 377-382 | 6 | 23 |
| α-helix | 395-400 | 6 | |
| α-helix | 412-414 | 3 | |
| α-helix | 416-425 | 10 | |
| α-helix | 426-430 | 5 | |
| α-helix | 431-453 | 23 | |
| α-helix | 463-466 | 4 | |
| α-helix | 469-499 | 31 | |
| α-helix | 505-508 | 4 | |
| α-helix | 511-531 | 21 | |
| α-helix | 537-550 | 14 | |
| α-helix | 551-556 | 6 | |
| α-helix | 560-572 | 13 | |
| α-helix | 573-577 | 5 | |
| α-helix | 578-598 | 21 | |
| α-helix | 630-641 | 12 | |
| α-helix | 659-681 | 23 | |
| α-helix | 688-711 | 24 | |
| β-strand | 726 | 1 | 24 |
| β-strand | 738 | 1 | 24 |
| β-strand | 742-747 | 6 | 23 |
Chain D: 31 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 146-148 | 3 | |
| α-helix | 157-163 | 7 | |
| β-strand | 166 | 1 | 25 |
| β-strand | 169 | 1 | 25 |
| α-helix | 171-183 | 13 | |
| α-helix | 187-190 | 4 | |
| α-helix | 204-210 | 7 | |
| α-helix | 214-222 | 9 | |
| α-helix | 234-236 | 3 | |
| α-helix | 251-257 | 7 | |
| α-helix | 261-268 | 8 | |
| α-helix | 287-293 | 7 | |
| α-helix | 299-319 | 21 | |
| α-helix | 325-327 | 3 | |
| α-helix | 336-343 | 8 | |
| α-helix | 346-352 | 7 | |
| α-helix | 363-365 | 3 | |
| β-strand | 368-373 | 6 | 26 |
| β-strand | 377-382 | 6 | 26 |
| α-helix | 395-400 | 6 | |
| α-helix | 412-414 | 3 | |
| α-helix | 416-425 | 10 | |
| α-helix | 426-430 | 5 | |
| α-helix | 431-453 | 23 | |
| α-helix | 463-466 | 4 | |
| α-helix | 469-499 | 31 | |
| α-helix | 503-508 | 6 | |
| α-helix | 511-531 | 21 | |
| α-helix | 537-550 | 14 | |
| α-helix | 551-556 | 6 | |
| α-helix | 560-598 | 39 | |
| α-helix | 630-641 | 12 | |
| α-helix | 659-680 | 22 | |
| α-helix | 681-684 | 4 | |
| α-helix | 689-711 | 23 | |
| β-strand | 726 | 1 | 27 |
| β-strand | 738 | 1 | 27 |
| β-strand | 742-747 | 6 | 26 |
Chain E: 3 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 11 |
| α-helix | 4 | 1 | |
| β-strand | 8 | 1 | 12 |
| α-helix | 14 | 1 | |
| β-strand | 15 | 1 | 11 |
| β-strand | 21-22 | 2 | 13 |
| β-strand | 30 | 1 | 12 |
| β-strand | 32-33 | 2 | 13 |
| α-helix | 38-40 | 3 | |
| β-strand | 45 | 1 | 14 |
| β-strand | 50 | 1 | 15 |
| β-strand | 57 | 1 | 14 |
| β-strand | 61-62 | 2 | 16 |
| β-strand | 70 | 1 | 15 |
| β-strand | 72-73 | 2 | 16 |
Chain F: 7 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2 | 1 | |
| β-strand | 3 | 1 | 5 |
| α-helix | 4 | 1 | |
| β-strand | 8 | 1 | 6 |
| α-helix | 14 | 1 | |
| β-strand | 15 | 1 | 5 |
| β-strand | 21-22 | 2 | 7 |
| β-strand | 30 | 1 | 6 |
| β-strand | 32-33 | 2 | 7 |
| α-helix | 38-40 | 3 | |
| β-strand | 45 | 1 | 8 |
| α-helix | 46 | 1 | |
| β-strand | 50 | 1 | 9 |
| α-helix | 56 | 1 | |
| β-strand | 57 | 1 | 8 |
| α-helix | 58 | 1 | |
| β-strand | 61-62 | 2 | 10 |
| β-strand | 70 | 1 | 9 |
| β-strand | 72-73 | 2 | 10 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Transient receptor potential cation channel subfamily V member 1 | A, B, C, D | protein | 637 | Rattus norvegicus | O35433 (AlphaFold model) |
| Tau-theraphotoxin-Hs1a | E, F | protein | 76 | Cyriopagopus schmidti | P0CH43 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>7L2T_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
GAMGSRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLN
LHNGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENG
ADVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVG
NTVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSG
KIGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSS
ETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYK
LKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFML
VSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVY
LVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYV
ILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQ
VGFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPG
Sequence of entity 2 (E, F), FASTA
>7L2T_2 Tau-theraphotoxin-Hs1a (chains E, F)
MDCAKEGEVCSWGKKCCDLDNFYCPMEFIPHCKKYKPYVPVTTNCAKEGEVCGWGSKCCH
GLDCPLAFIPYCEKYR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 65I | (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapenta… | C22 H44 N O8 P | 4 |
| XJ7 | (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydrox… | C26 H49 O13 P | 4 |
Water and common crystallization additives (NA) are not listed.
Primary citation
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Zhang, K., Julius, D., Cheng, Y. Cell (2021) 184:5138-5150.e12. DOI 10.1016/j.cell.2021.08.012 · PubMed
Other PDB entries of the same protein (UniProt O35433 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3SUI 1.95 Å, Crystal structure of ca2+-calmodulin in complex with a trpv1 c-terminal peptide
- 8U4D 2.2 Å, TRPV1 in nanodisc bound with PI-Br4, consensus structure
- 8U3A 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
- 8U3C 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer)
- 8U43 2.4 Å, TRPV1 in nanodisc bound with PIP2-Br4
- 7L2P 2.6 Å, cryo-EM structure of unliganded minimal TRPV1
- 7L2H 2.63 Å, Cryo-EM structure of unliganded full-length TRPV1 at neutral pH
- 7LP9 2.63 Å, Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius
- 2PNN 2.7 Å, Crystal Structure of the Ankyrin Repeat Domain of Trpv1
- 9W4M 2.7 Å, ratTRPV1 bound with antagonist AMG517
- 7L2S 2.71 Å, cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound state
- 7MZ5 2.76 Å, Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state
Browse structure collections
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