8U4D: TRPV1 in nanodisc

TRPV1 in nanodisc bound with PI-Br4, consensus structure. Determined by electron microscopy at 2.2 Å resolution. Released 8 May 2024.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 18,311
Mol. weight: 296.31 kDa
Ligands: VPN
Released: 8 May 2024

Explore 8U4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U4D contains 120 α-helices and 24 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 A, B, C and D: 30 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	193	1	1
β-strand	203	1	1
α-helix	204-210	7
α-helix	214-222	9
α-helix	234-236	3
α-helix	251-257	7
α-helix	261-268	8
α-helix	287-294	8
α-helix	299-319	21
α-helix	325-327	3
α-helix	336-343	8
α-helix	346-353	8
α-helix	363-365	3
β-strand	368-374	7	2
β-strand	377-383	7	2
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	463-464	2
α-helix	469-499	31
α-helix	505-508	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	578-598	21
α-helix	630-641	12
α-helix	656-667	12
α-helix	668-675	8
α-helix	676-688	13
α-helix	690-710	21
β-strand	723-730	8	2
β-strand	736-747	12	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 1	A, B, C, D	protein	635	Rattus norvegicus	O35433 (AlphaFold model)

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

>8U4D_1 Transient receptor potential cation channel subfamily V member 1 (chains A, B, C, D)
MGSRLYDRRSIFDAVAQSNCQELESLLPFLQRSKKRLTDSEFKDPETGKTCLLKAMLNLH
NGQNDTIALLLDVARKTDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVENGAD
VQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNT
VLHALVEVADNTVDNTKFVTSMYNEILILGAKLHPTLKLEEITNRKGLTPLALAASSGKI
GVLAYILQREIHEPECRHLSRKFTEWAYGPVHSSLYDLSCIDTCEKNSVLEVIAYSSSET
PNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLK
NTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVS
VVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLV
FLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVIL
TYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRKAFRSGKLLQVG
FTPDGKDDYRWCFRVDEVNWTTWNTNVGIINEDPG

Ligands and cofactors

ID	Name	Formula	Copies
VPN	(2S)-2-[(9,10-dibromooctadecanoyl)oxy]-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3…	C45 H83 Br4 O13 P	4

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
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
9W4T 2.87 Å, ratTRPV1 bound with antagonist AMG9810

Browse structure collections

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