8U3C: TRPV1 in nanodisc

TRPV1 in nanodisc bound with PI-Br4 bound in Conformation 2 (monomer). Determined by electron microscopy at 2.3 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 3,459
Mol. weight: 188.01 kDa
Ligands: 3PH, PCW, VPN
Released: 8 May 2024

Explore 8U3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U3C contains 27 α-helices and 2 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 0 β-strands

Element	Residues	Length
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	462-466	5
α-helix	469-499	31
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	578-592	15
α-helix	630-639	10
α-helix	640-642	3
α-helix	660-667	8
α-helix	668-674	7
α-helix	675-688	14
α-helix	690-710	21

Chain D: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	561-572	12
α-helix	573-577	5
α-helix	578-598	21
β-strand	599	1	1
α-helix	630-641	12
β-strand	653	1	1
α-helix	656-667	12
α-helix	668-674	7
α-helix	675-688	14
α-helix	690-702	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, D	protein	815	Rattus norvegicus	O35433 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8U3C_1 Transient receptor potential cation channel subfamily V member 1 (chains A, D)
MEQRASLDSEESESPPQENSCLDPPDRDPNCKPPPVKPHIFTTRSRTRLFGKGDSEEASP
LDCPYEEGGLASCPIITVSSVLTIQRPGDGPASVRPSSQDSVSAGEKPPRLYDRRSIFDA
VAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLHNGQNDTIALLLDVA
RKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGADVQAAANGDFFKKTK
GRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVD
NTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKIGVLAYILQREIHEP
ECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSETPNRHDMLLVEPLNR
LLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEIL
SVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVAS
MVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIE
DGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMG
ETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQVGFTPDGKDDYRWCFR
VDEVNWTTWNTNVGIINEDPGNCEGVKRTLSFSLRSGRVSGRNWKNFALVPLLRDASTRD
RHATQQEEVQLKHYTGSLKPEDAEVFKDSMVPGEK

Ligands and cofactors

ID	Name	Formula	Copies
3PH	1,2-diacyl-glycerol-3-sn-phosphate	C39 H77 O8 P	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	1
VPN	(2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3…	C45 H83 Br4 O13 P	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural basis of TRPV1 modulation by endogenous bioactive lipids. Arnold, W.R., Mancino, A., Moss 3rd, F.R. et al. Nat Struct Mol Biol (2024) 31:1377-1385. DOI 10.1038/s41594-024-01299-2 · 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)
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
9W4T 2.87 Å, ratTRPV1 bound with antagonist AMG9810

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