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7l2v

cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state b

Method: ELECTRON MICROSCOPY Dmax: 128.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transient receptor potential cation channel subfamily V member 1

Rattus norvegicus

UniProt O35433

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 110–764 Chain B； UniProt 110–764 Chain C； UniProt 110–764 Chain D； UniProt 110–764 Not recorded 6EU resiniferatoxin × 4 XPS 6-deoxy-6-(methylamino)-D-galactitol × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 6.82 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.64 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7L2V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2NYJ Crystal structure of the ankyrin repeat domain of TRPV1 Deposited 2006-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 101–364（264 aa） Fragment：ankyrin repeart domain, residues 101-365
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.033MM PROTEIN, 5% PEG8000, 0.1M SODIUM CITRATE, 5MM ATP, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.286
2PNN Crystal Structure of the Ankyrin Repeat Domain of Trpv1 Deposited 2007-04-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 101–364（264 aa） Fragment：Ankyrin Repeat Domain
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；3% PEG 8000, 0.1M SODIUM CITRATE, 5MM ATP, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K, pH 5.00
Resolution 2.70 Å R-free 0.248
3J5P Structure of TRPV1 ion channel determined by single particle electron cryo-microscopy Deposited 2013-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 111–603（493 aa） Fragment：SEE REMARK 999
Chain A 626–718（93 aa） Fragment：SEE REMARK 999
Chain B 111–603（493 aa） Fragment：SEE REMARK 999
Chain B 626–718（93 aa） Fragment：SEE REMARK 999
Chain C 111–603（493 aa） Fragment：SEE REMARK 999
Chain C 626–718（93 aa） Fragment：SEE REMARK 999
Chain D 111–603（493 aa） Fragment：SEE REMARK 999
Chain D 626–718（93 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 150 mM NaCl, 20 mM HEPES, 2 mM TCEP；pH 7.4；150 mM NaCl, 20 mM HEPES, 2 mM TCEP
cryo-EM vitrification conditions Blot for 6 sec；120 K；Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)
Resolution 3.27 Å
3J5Q Structure of TRPV1 ion channel in complex with DkTx and RTX determined by single particle electron cryo-microscopy Deposited 2013-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 111–719（609 aa） Fragment：SEE REMARK 999
Chain D 111–719（609 aa） Fragment：SEE REMARK 999
Chain E 111–719（609 aa） Fragment：SEE REMARK 999
Chain G 111–719（609 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 150 mM NaCl, 20 mM HEPES, 2 mM TCEP；pH 7.4；150 mM NaCl, 20 mM HEPES, 2 mM TCEP
cryo-EM vitrification conditions Blot for 6 sec；120 K；Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)
Resolution 3.80 Å
3J5R Reconstruction of TRPV1 ion channel in complex with capsaicin by single particle cryo-microscopy Deposited 2013-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 111–603（493 aa） Fragment：SEE REMARK 999
Chain A 626–718（93 aa） Fragment：SEE REMARK 999
Chain B 111–603（493 aa） Fragment：SEE REMARK 999
Chain B 626–718（93 aa） Fragment：SEE REMARK 999
Chain C 111–603（493 aa） Fragment：SEE REMARK 999
Chain C 626–718（93 aa） Fragment：SEE REMARK 999
Chain D 111–603（493 aa） Fragment：SEE REMARK 999
Chain D 626–718（93 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 150 mM NaCl, 20 mM HEPES, 2 mM TCEP；pH 7.4；150 mM NaCl, 20 mM HEPES, 2 mM TCEP
cryo-EM vitrification conditions Blot for 6 sec；120 K；Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III)
Resolution 4.20 Å
3J9J Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy Deposited 2015-02-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 111–603（493 aa） Fragment：SEE REMARK 999
Chain A 627–719（93 aa） Fragment：SEE REMARK 999
Chain B 111–603（493 aa） Fragment：SEE REMARK 999
Chain B 627–719（93 aa） Fragment：SEE REMARK 999
Chain C 111–603（493 aa） Fragment：SEE REMARK 999
Chain C 627–719（93 aa） Fragment：SEE REMARK 999
Chain D 111–603（493 aa） Fragment：SEE REMARK 999
Chain D 627–719（93 aa） Fragment：SEE REMARK 999
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
3SUI Crystal structure of ca2+-calmodulin in complex with a trpv1 c-terminal peptide Deposited 2011-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 767–801（35 aa） Fragment：Unp residues 767-801
Not recorded CA CALCIUM ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES PH6.0, 2.2-2.8M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Resolution 1.95 Å R-free 0.248
5IRX Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc Deposited 2016-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain A 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain B 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain B 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain C 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain C 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain D 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain D 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Not recorded 6O8 (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium × 4 6OE (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate × 8 6EU resiniferatoxin × 4 6O9 (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Resolution 2.95 Å
5IRZ Structure of TRPV1 determined in lipid nanodisc Deposited 2016-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain B 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain C 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain C 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain D 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain D 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain E 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain E 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Not recorded 6O8 (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium × 4 6ES (2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(pentanoyloxy)propan-2-yl decanoate × 4 6OE (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Resolution 3.28 Å
5IS0 Structure of TRPV1 in complex with capsazepine, determined in lipid nanodisc Deposited 2016-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain B 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain C 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain C 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain D 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain D 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Chain E 110–603（494 aa） Fragment：UNP residues 110-603, 627-764
Chain E 627–764（138 aa） Fragment：UNP residues 110-603, 627-764
Not recorded 6ET capsazepine × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 6 seconds before plunging into liquid ethane (FEI VITROBOT MARK III).
Resolution 3.43 Å
7L2H Cryo-EM structure of unliganded full-length TRPV1 at neutral pH Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 XJD (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl tridecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
7L2I Cryo-EM structure of full-length TRPV1 at pH6a state Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded XJA (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7L2J Cryo-EM structure of full-length TRPV1 at pH6c state Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.66 Å
7L2K Cryo-EM structure of full-length TRPV1 at pH6b state Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.89 Å
7L2L Cryo-EM structure of RTX-bound full-length TRPV1 in O1 state Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded 6EU resiniferatoxin × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7L2M Cryo-EM structure of DkTx/RTX-bound full-length TRPV1 Deposited 2020-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded 6EU resiniferatoxin × 4 NA SODIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
7L2N Cryo-EM structure of RTX-bound full-length TRPV1 in C1 state Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded 6EU resiniferatoxin × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7L2O Cryo-EM structure of RTX-bound full-length TRPV1 at pH 5.5 Deposited 2020-12-17 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded 6EU resiniferatoxin × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
7L2P cryo-EM structure of unliganded minimal TRPV1 Deposited 2020-12-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 6IY (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7L2R Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state Deposited 2020-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7L2S cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound state Deposited 2020-12-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 6IY (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.71 Å
7L2T cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state Deposited 2020-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 NA SODIUM ION × 1 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
7L2U cryo-EM structure of DkTx-bound minimal TRPV1 in open state Deposited 2020-12-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 XKP (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
7L2W cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state a Deposited 2020-12-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded 6EU resiniferatoxin × 4 6IY (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.82
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
7L2X cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state c Deposited 2020-12-17 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded 6EU resiniferatoxin × 4 6IY (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate × 4 XPJ 1-deoxy-1-(methylamino)-D-allitol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.82
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
7LP9 Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded T7X Phosphatidylinositol × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 28 NA SODIUM ION × 2 YFP 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
7LPA Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees Celsius Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 12 4DY (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide × 4 YFP 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
7LPB Cryo-EM structure of full-length TRPV1 with capsaicin at 25 degrees Celsius Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 12 YFP 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol × 4 4DY (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
7LPC Cryo-EM structure of full-length TRPV1 at 48 degrees Celsius Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 24 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 YFP 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol × 4 T7X Phosphatidylinositol × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
7LPD Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an intermediate state, class 2 Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 12 4DY (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
7LPE Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an open state, class 1 Deposited 2021-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 4 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 4 4DY (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
7MZ5 Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–838（837 aa）
Chain B 2–838（837 aa）
Chain C 2–838（837 aa）
Chain D 2–838（837 aa）
Not recorded 6EU resiniferatoxin × 4 NA SODIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
7MZ6 Cryo-EM structure of minimal TRPV1 with 1 perturbed PI Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 4 6IY (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7MZ7 Cryo-EM structure of minimal TRPV1 with 4 partially bound RTX Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded 6EU resiniferatoxin × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.35 Å
7MZ9 Cryo-EM structure of minimal TRPV1 with 1 partially bound RTX Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded 6EU resiniferatoxin × 1 XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 3 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
7MZA Cryo-EM structure of minimal TRPV1 with 2 bound RTX in adjacent pockets Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 2 6EU resiniferatoxin × 2 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
7MZB Cryo-EM structure of minimal TRPV1 with 3 bound RTX and 1 perturbed PI Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 1 6EU resiniferatoxin × 3 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
7MZC Cryo-EM structure of minimal TRPV1 with RTX bound in C1 state Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded 6EU resiniferatoxin × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7MZD Cryo-EM structure of minimal TRPV1 with RTX bound in C2 state Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded 6EU resiniferatoxin × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.3
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7MZE Cryo-EM structure of minimal TRPV1 with 2 bound RTX in opposite pockets Deposited 2021-05-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa） Fragment：UNP residues 110-764
Chain B 110–764（655 aa） Fragment：UNP residues 110-764
Chain C 110–764（655 aa） Fragment：UNP residues 110-764
Chain D 110–764（655 aa） Fragment：UNP residues 110-764
Not recorded XJ7 (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate × 2 NA SODIUM ION × 1 6EU resiniferatoxin × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.85
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.42 Å
7RQU Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in a closed state, class I Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 6EU resiniferatoxin × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 20 YFP 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
7RQV Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an intermediate-closed state, class II Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 4 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 12 6EU resiniferatoxin × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
7RQW Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an open state, class III Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 6EU resiniferatoxin × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 4 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
7RQX Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an intermediate-open state, class A Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 12 6EU resiniferatoxin × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
7RQY Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an open state, class B Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 6EU resiniferatoxin × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 4 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
7RQZ Cryo-EM structure of the full-length TRPV1 with RTx at 48 degrees Celsius, in an open state, class alpha Deposited 2021-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 6EU resiniferatoxin × 4 LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 8 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8T0C TRPV1 in Nanodisc bound with lysophosphatidic acid in all four monomers Deposited 2023-05-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8T0E TRPV1 in Nanodisc not bound with lysophosphatidic acid (apo) Deposited 2023-05-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa） Fragment：truncated construct
Chain B 1–838（838 aa） Fragment：truncated construct
Chain C 1–838（838 aa） Fragment：truncated construct
Chain D 1–838（838 aa） Fragment：truncated construct
Not recorded 8IJ (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8T0Y TRPV1 in nanodisc bound with one LPA in one monomer Deposited 2023-06-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa） Fragment：truncated construct
Chain B 1–838（838 aa） Fragment：truncated construct
Chain C 1–838（838 aa） Fragment：truncated construct
Chain D 1–838（838 aa） Fragment：truncated construct
Not recorded 8IJ (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate × 3 NA SODIUM ION × 1 NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8T10 TRPV1 in nanodisc bound with two LPA molecules in opposite monomers Deposited 2023-06-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa） Fragment：truncated construct
Chain B 1–838（838 aa） Fragment：truncated construct
Chain C 1–838（838 aa） Fragment：truncated construct
Chain D 1–838（838 aa） Fragment：truncated construct
Not recorded 8IJ (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate × 2 NA SODIUM ION × 2 NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8T3L TRPV1 in nanodisc bound with 2 LPA molecules in neighboring monomers Deposited 2023-06-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded 8IJ (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate × 2 NA SODIUM ION × 2 NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8T3M TRPV1 in nanodisc bound with 3 LPA molecules Deposited 2023-06-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded 85R [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate × 1 NA SODIUM ION × 2 NKN (2R)-2-hydroxy-3-(phosphonooxy)propyl tetradecanoate × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8U2Z TRPV1 in nanodisc bound with diC8-PIP2 in the dilated state Deposited 2023-09-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 CLR CHOLESTEROL × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8U30 TRPV1 in nanodisc bound with diC8-PIP2 in the closed state Deposited 2023-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8U3A TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer) Deposited 2023-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded VPN (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8U3C TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer) Deposited 2023-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded VPN (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.30 Å
8U3J TRPV1 in nanodisc bound with empty vanilloid binding pocket at 4C Deposited 2023-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 197–753（557 aa）
Chain B 197–753（557 aa）
Chain C 197–753（557 aa）
Chain D 197–753（557 aa）
Not recorded 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8U3L TRPV1 in nanodisc bound with empty vanilloid binding pocket at 25C Deposited 2023-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8U43 TRPV1 in nanodisc bound with PIP2-Br4 Deposited 2023-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded V5H (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8U4D TRPV1 in nanodisc bound with PI-Br4, consensus structure Deposited 2023-09-10 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 110–764（655 aa）
Chain B 110–764（655 aa）
Chain C 110–764（655 aa）
Chain D 110–764（655 aa）
Not recorded VPN (2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9R,10S)-9,10-dibromooctadecanoate × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9ISG Structure of rat TRPV1 in complex with PSFL426-S5 Deposited 2024-07-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded A1D92 4-azanyl-3-sulfanylidene-1,2,4-triazine-5,6-dione × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9OGK Refinement of PDB-3J5R against EMD-8117 using EMAN2 Deposited 2025-04-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9W4M ratTRPV1 bound with antagonist AMG517 Deposited 2025-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded A1D6R ~{N}-[4-[6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl]oxy-1,3-benzothiazol-2-yl]ethanamide × 4 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9W4N Structure of rat TRPV1 in complex with SB-366791 Deposited 2025-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded ZEI (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Hepes, 150 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9W4T ratTRPV1 bound with antagonist AMG9810 Deposited 2025-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–838（838 aa）
Chain B 1–838（838 aa）
Chain C 1–838（838 aa）
Chain D 1–838（838 aa）
Not recorded A1D6W (~{Z})-3-(4-~{tert}-butylphenyl)-~{N}-(2,3-dihydro-1,4-benzodioxin-6-yl)prop-2-enamide × 4 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å

65 other PDB entries and 65 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRPV1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–637； UniProt 110–764 Author chain B； PDBConstruct 6–637； UniProt 110–764 Author chain C； PDBConstruct 6–637； UniProt 110–764 Author chain D； PDBConstruct 6–637； UniProt 110–764

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7l2v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7l2v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7l2v
Deposition date deposition_date2020-12-17
Structure title titlecryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state b
Keywords keywordsTRP channel, cryo-EM, nanodisc, large cation, vanilloid agonist, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.76 Å
Radius of gyration Rg (electron density) rg_electron43.83 Å
Forward intensity I(0) i0784501000.00
Molecular weight molecular_weight249330.0 kDa
Excluded volume excluded_volume319060 ų
Envelope volume envelope_volume451630 ų
Hydration-shell volume shell_volume82918 ų
Envelope diameter envelope_diameter137.9 Å
Shell Rg shell_rg51.95 Å
Envelope Rg envelope_rg42.40 Å
Shape Rg shape_rg43.85 Å
Total Rg total_rg44.12 Å
Total atoms total_atoms17594
Residues n_residues2144
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax128.7 Å
Rg (real space) rg_real44.38 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real7.8450e+08
I(0) uncertainty (real space) i0_real_error1.3510e+07
Rg (reciprocal space) rg_reciprocal44.76 Å
I(0) (reciprocal space) i0_reciprocal784800000.0000
Solution quality estimate total_estimate0.8813
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.5 Å
Skewness Skewness skewness-0.056
Kurtosis Kurtosis kurtosis-0.531
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51310000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.647
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)