5IRX: TRPV1

Structure of TRPV1 in complex with DkTx and RTX, determined in lipid nanodisc. Determined by electron microscopy at 2.95 Å resolution. Released 25 May 2016.

Method: Electron microscopy
Resolution: 2.95 Å
Organisms: Rattus norvegicus, Haplopelma schmidti
Chains: 6
Atoms: 13,162
Mol. weight: 317.88 kDa
Ligands: 6O9, 6EU, 6OE, 6O8
Released: 25 May 2016

Explore 5IRX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IRX contains 94 α-helices and 60 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, C and D: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	336-341	6
α-helix	346-353	8
β-strand	369-374	6	1
β-strand	377-381	5	1
α-helix	395-400	6
α-helix	412-415	4
α-helix	419-425	7
α-helix	426-430	5
α-helix	431-453	23
α-helix	462-463	2
α-helix	469-498	30
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-554	4
β-strand	557	1	2
β-strand	559	1	2
α-helix	564-571	8
α-helix	572-577	6
α-helix	578-580	3
α-helix	584-598	15
α-helix	630-641	12
α-helix	656-667	12
α-helix	668-674	7
α-helix	675-691	17
α-helix	693-712	20
α-helix	716-719	4
β-strand	724-725	2	3
β-strand	739-740	2	3
β-strand	743-746	4	1

Chains E and F: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	13
β-strand	5	1	14
β-strand	7	1	14
β-strand	8	1	15
β-strand	15	1	13
β-strand	22	1	16
β-strand	30	1	15
β-strand	32	1	16
α-helix	33-36	4
β-strand	45	1	17
β-strand	50	1	18
β-strand	51	1	19
β-strand	55	1	19
β-strand	57	1	17
β-strand	62	1	20
α-helix	69	1
β-strand	70	1	18
α-helix	71	1
β-strand	72	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	protein	636	Rattus norvegicus	O35433 (AlphaFold model)
Tau-theraphotoxin-Hs1a	E, F	protein	75	Haplopelma schmidti	P0CH43 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5IRX_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
AMGSRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNL
HNGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGA
DVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGN
TVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGK
IGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSE
TPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKL
KNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLV
SVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYL
VFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVI
LTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQV
GFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPG

Sequence of entity 2 (E, F), FASTA

>5IRX_2 Tau-theraphotoxin-Hs1a (chains E, F)
DCAKEGEVCSWGKKCCDLDNFYCPMEFIPHCKKYKPYVPVTTNCAKEGEVCGWGSKCCHG
LDCPLAFIPYCEKYR

Ligands and cofactors

ID	Name	Formula	Copies
6O9	(2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl…	C12 H24 N O8 P	4
6EU	resiniferatoxin	C37 H40 O9	4
6OE	(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl…	C17 H34 N O8 P	8
6O8	(4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trio…	C19 H39 N O8 P	4

Primary citation

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Gao, Y., Cao, E., Julius, D. et al. Nature (2016) 534:347-351. DOI 10.1038/nature17964 · PubMed

Other PDB entries of the same protein (UniProt O35433 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SUI 1.95 Å, Crystal structure of ca2+-calmodulin in complex with a trpv1 c-terminal peptide
8U4D 2.2 Å, TRPV1 in nanodisc bound with PI-Br4, consensus structure
8U3A 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 1 (monomer)
8U3C 2.3 Å, TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer)
8U43 2.4 Å, TRPV1 in nanodisc bound with PIP2-Br4
7L2P 2.6 Å, cryo-EM structure of unliganded minimal TRPV1
7L2H 2.63 Å, Cryo-EM structure of unliganded full-length TRPV1 at neutral pH
7LP9 2.63 Å, Cryo-EM structure of full-length TRPV1 at 4 degrees Celsius
2PNN 2.7 Å, Crystal Structure of the Ankyrin Repeat Domain of Trpv1
9W4M 2.7 Å, ratTRPV1 bound with antagonist AMG517
7L2S 2.71 Å, cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound state
7MZ5 2.76 Å, Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state

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