5IRZ: TRPV1 determined in lipid nanodisc

Structure of TRPV1 determined in lipid nanodisc. Determined by electron microscopy at 3.28 Å resolution. Released 25 May 2016.

Method: Electron microscopy
Resolution: 3.28 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 12,504
Mol. weight: 302.47 kDa
Ligands: 6O8, 6ES, 6OE
Released: 25 May 2016

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

Secondary structure: helices and β-sheets

5IRZ contains 84 α-helices and 28 β-strands across 4 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 B, C, D and E: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	336-343	8
α-helix	346-352	7
β-strand	368-369	2	7
β-strand	373	1	8
β-strand	378	1	8
β-strand	380-382	3	7
α-helix	395-400	6
α-helix	412-414	3
α-helix	416-425	10
α-helix	426-430	5
α-helix	431-453	23
α-helix	475-496	22
α-helix	506-509	4
α-helix	511-531	21
α-helix	537-550	14
α-helix	551-556	6
α-helix	560-572	13
α-helix	573-577	5
α-helix	578-596	19
β-strand	599	1	9
α-helix	603-628	3
α-helix	630-642	13
β-strand	653	1	9
α-helix	656-666	11
α-helix	667-674	8
α-helix	675-688	14
α-helix	692-709	18
β-strand	744-745	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	B, C, D, E	protein	636	Rattus norvegicus	O35433 (AlphaFold model)

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

>5IRZ_1 Transient receptor potential cation channel subfamily V member 1 (chains B, C, D, E)
AMGSRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNL
HNGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGA
DVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGN
TVLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGK
IGVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSE
TPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKL
KNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLV
SVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYL
VFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVI
LTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQV
GFTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPG

Ligands and cofactors

ID	Name	Formula	Copies
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
6ES	(2S)-1-{[(R)-hydroxy{[(1R,2R,3S,4S,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}…	C24 H45 O13 P	4
6OE	(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl…	C17 H34 N O8 P	16

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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