3j9j

Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy

Method: ELECTRON MICROSCOPY D_max: 108.0 Å Quality: REASONABLE

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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

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 111–603 Chain A； UniProt 627–719 Chain B； UniProt 111–603 Chain B； UniProt 627–719 Chain C； UniProt 111–603 Chain C； UniProt 627–719 Chain D； UniProt 111–603 Chain D； UniProt 627–719	Fragment：SEE REMARK 999	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.27 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 3J9J	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 experimental conditions	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 mutation/modification Different oligomeric state 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 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
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 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 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 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 mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification 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 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 construct Different mutation/modification 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	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 mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification 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	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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
7L2V cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state b Deposited 2020-12-17	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 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 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
7L2W cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state a Deposited 2020-12-17	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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 1–493； UniProt 111–603 Author chain A； PDBConstruct 494–586； UniProt 627–719 Author chain B； PDBConstruct 1–493； UniProt 111–603 Author chain B； PDBConstruct 494–586； UniProt 627–719 Author chain C； PDBConstruct 1–493； UniProt 111–603 Author chain C； PDBConstruct 494–586； UniProt 627–719 Author chain D； PDBConstruct 1–493； UniProt 111–603 Author chain D； PDBConstruct 494–586； UniProt 627–719

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j9j
Deposition date deposition_date	2015-02-02
Structure title title	Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy
Keywords keywords	alpha helical, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.29 Å
Radius of gyration Rg (electron density) rg_electron	35.23 Å
Forward intensity I(0) i0	272214000.00
Molecular weight molecular_weight	148160.0 kDa
Excluded volume excluded_volume	191290 Å³
Envelope volume envelope_volume	241980 Å³
Hydration-shell volume shell_volume	55340 Å³
Envelope diameter envelope_diameter	115.8 Å
Shell Rg shell_rg	43.15 Å
Envelope Rg envelope_rg	35.47 Å
Shape Rg shape_rg	35.23 Å
Total Rg total_rg	35.84 Å
Total atoms total_atoms	21068
Residues n_residues	1260
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	108.0 Å
Rg (real space) rg_real	36.05 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	2.7220e+08
I(0) uncertainty (real space) i0_real_error	4.1730e+06
Rg (reciprocal space) rg_reciprocal	36.20 Å
I(0) (reciprocal space) i0_reciprocal	272300000.0000
Solution quality estimate total_estimate	0.6659
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	49.1 Å
Skewness Skewness skewness	0.082
Kurtosis Kurtosis kurtosis	-0.434
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	45130000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.978; Smooth: 0.814

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.27 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	35645

Description description	Transient receptor potential cation channel subfamily V member 1
Molecular weight formula_weight	67235.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21068

Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy

1. Protein Identity and Related Structures Protein Identity & Related Structures

Transient receptor potential cation channel subfamily V member 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Homo sapiens

fit	/app/data/saxs_computation/j9/3j9j/3j9j.fit
pddf	/app/data/pr_computation/j9/3j9j/3j9j.pr.out
profile	/app/data/saxs_computation/j9/3j9j/3j9j.dat