9JDM: Human TRPV3 determined in MSP2N2 nanodisc

Cryo-EM structure of human TRPV3 determined in MSP2N2 nanodisc. Determined by electron microscopy at 3.13 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 3.13 Å
Organism: Homo sapiens
Chains: 4
Atoms: 20,992
Mol. weight: 388.27 kDa
Ligands: POV
Released: 26 Mar 2025

Explore 9JDM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JDM contains 120 α-helices and 36 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	120-126	7
α-helix	134-145	12
β-strand	163	1	1
β-strand	170	1	1
α-helix	171-177	7
α-helix	183-196	14
α-helix	201-204	4
α-helix	218-224	7
α-helix	228-236	9
α-helix	265-271	7
α-helix	275-282	8
α-helix	299-305	7
α-helix	316-328	13
α-helix	344-351	8
α-helix	354-361	8
β-strand	376-382	7	2
β-strand	385-390	6	2
α-helix	403-409	7
α-helix	416-419	4
α-helix	423-432	10
α-helix	433-437	5
α-helix	438-460	23
α-helix	484-506	23
α-helix	521-541	21
α-helix	548-561	14
α-helix	562-568	7
α-helix	570-585	16
α-helix	587-605	19
α-helix	606-608	3
β-strand	609	1	3
α-helix	625-636	12
β-strand	648	1	3
α-helix	651-662	12
α-helix	663-669	7
α-helix	670-686	17
α-helix	691-706	16
β-strand	717	1	4
β-strand	731	1	4
β-strand	733-737	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 3	A, B, C, D	protein	799	Homo sapiens	Q8NET8 (AlphaFold model)

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

>9JDM_1 Transient receptor potential cation channel subfamily V member 3 (chains A, B, C, D)
MKAHPKEMVPLMGKRVAAPSGNPAVLPEKRPAEITPTKKSAHFFLEIEGFEPNPTVAKTS
PPVFSKPMDSNIRQCISGNCDDMDSPQSPQDDVTETPSNPNSPSAQLAKEEQRRKKRRLK
KRIFAAVSEGCVEELVELLVELQELCRRRHDEDVPDFLMHKLTASDTGKTCLMKALLNIN
PNTKEIVRILLAFAEENDILGRFINAEYTEEAYEGQTALNIAIERRQGDIAALLIAAGAD
VNAHAKGAFFNPKYQHEGFYFGETPLALAACTNQPEIVQLLMEHEQTDITSRDSRGNNIL
HALVTVAEDFKTQNDFVKRMYDMILLRSGNWELETTRNNDGLTPLQLAAKMGKAEILKYI
LSREIKEKRLRSLSRKFTDWAYGPVSSSLYDLTNVDTTTDNSVLEITVYNTNIDNRHEML
TLEPLHTLLHMKWKKFAKHMFFLSFCFYFFYNITLTLVSYYRPREEEAIPHPLALTHKMG
WLQLLGRMFVLIWAMCISVKEGIAIFLLRPSDLQSILSDAWFHFVFFIQAVLVILSVFLY
LFAYKEYLACLVLAMALGWANMLYYTRGFQSMGMYSVMIQKVILHDVLKFLFVYIVFLLG
FGVALASLIEKCPKDNKDCSSYGSFSDAVLELFKLTIGLGDLNIQQNSKYPILFLFLLIT
YVILTFVLLLNMLIALMGETVENVSKESERIWRLQRARTILEFEKMLPEWLRSRFRMGEL
CKVAEDDFRLCLRINEVKWTEWKTHVSFLNEDPGPVRRTDFNKIQDSSRNNSKTTLNAFE
EVEEFPETSVSNSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	28

Primary citation

Plant essential oil targets TRPV3 for skin renewal and structural mechanism of action. Li, Y., Lu, X., Cheng, X. et al. Nat Commun (2025) 16:2728-2728. DOI 10.1038/s41467-025-58033-9 · PubMed

Other PDB entries of the same protein (UniProt Q8NET8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6H9J 1.83 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (229-255)
6HA6 1.98 Å, Factor Inhibiting HIF (FIH) in complex with zinc, NOG and TRPV3 (220-246)
7QQN 2.45 Å, The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3
8V6K 2.46 Å, Apo-state cryo-EM structure of human TRPV3 in cNW30 nanodiscs
13LU 2.49 Å, Structure of human TRPV3-W521S Olmsted syndrome mutant in the closed state
7XJ0 2.53 Å, Structure of human TRPV3 in complex with Trpvicin
8GKA 2.55 Å, Human TRPV3 tetramer structure, closed conformation
8V6N 2.59 Å, Open-state cryo-EM structure of human TRPV3 in presence of 2-APB in cNW30 nanodiscs
9PJ5 2.76 Å, Closed-state structure of wild-type human TRPV3 purified in GDN detergent
8V6O 2.83 Å, Inactivated-state cryo-EM structure of human TRPV3 in presence of 2-APB in cNW30 nanodiscs
13LJ 2.86 Å, Structure of human TRPV3-G568C Olmsted syndrome mutant in the closed state
7XJ1 2.93 Å, Structure of human TRPV3_G573S in complex with Trpvicin in C2 symmetry

Browse structure collections

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