8V6O: PDB entry 8V6O

Inactivated-state cryo-EM structure of human TRPV3 in presence of 2-APB in cNW30 nanodiscs. Determined by electron microscopy at 2.83 Å resolution. Released 17 Apr 2024.

Method: Electron microscopy
Resolution: 2.83 Å
Organism: Homo sapiens
Chains: 4
Atoms: 22,683
Mol. weight: 396.91 kDa
Ligands: FZ4, POV
Released: 17 Apr 2024

Explore 8V6O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V6O contains 144 α-helices and 32 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: 36 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	118-129	12
α-helix	132-144	13
α-helix	154-162	9
α-helix	171-177	7
α-helix	185-196	12
α-helix	200-204	5
β-strand	208	1	1
β-strand	214	1	1
α-helix	218-224	7
α-helix	228-237	10
α-helix	265-271	7
α-helix	275-283	9
α-helix	299-305	7
α-helix	316-328	13
α-helix	344-351	8
α-helix	354-361	8
α-helix	371-373	3
β-strand	376-382	7	2
β-strand	385-391	7	2
α-helix	403-408	6
α-helix	416-419	4
α-helix	423-432	10
α-helix	433-437	5
α-helix	438-457	20
α-helix	470-471	2
α-helix	481-504	24
α-helix	516-519	4
α-helix	522-541	20
α-helix	547-560	14
α-helix	561-568	8
α-helix	570-581	12
α-helix	582-586	5
α-helix	587-605	19
β-strand	609	1	3
α-helix	610-611	2
α-helix	612-614	3
α-helix	624-637	14
α-helix	643-646	4
β-strand	648	1	3
α-helix	651-676	26
α-helix	682-706	25
α-helix	709-712	4
β-strand	719-724	6	2
β-strand	727-737	11	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 3	A, B, C, D	protein	808	Homo sapiens	Q8NET8 (AlphaFold model)

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

>8V6O_1 Transient receptor potential cation channel subfamily V member 3 (chains A, B, C, D)
MKAHPKEMVPLMGKRVAAPSGNPAILPEKRPAEITPTKKSAHFFLEIEGFEPNPTVAKTS
PPVFSKPMDSNIRQCISGNCDDMDSPQSPQDDVTETPSNPNSPSAQLAKEEQRRKKRRLK
KRIFAAVSEGCVEELVELLVELQELCRRRHDEDVPDFLMHKLTASDTGKTCLMKALLNIN
PNTKEIVRILLAFAEENDILGRFINAEYTEEAYEGQTALNIAIERRQGDIAALLIAAGAD
VNAHAKGAFFNPKYQHEGFYFGETPLALAACTNQPEIVQLLMEHEQTDITSRDSRGNNIL
HALVTVAEDFKTQNDFVKRMYDMILLRSGNWELETTRNNDGLTPLQLAAKMGKAEILKYI
LSREIKEKRLRSLSRKFTDWAYGPVSSSLYDLTNVDTTTDNSVLEITVYNTNIDNRHEML
TLEPLHTLLHMKWKKFAKHMFFLSFCFYFFYNITLTLVSYYRPREEEAIPHPLALTHKMG
WLQLLGRMFVLIWAMCISVKEGIAIFLLRPSDLQSILSDAWFHFVFFIQAVLVILSVFLY
LFAYKEYLACLVLAMALGWANMLYYTRGFQSMGMYSVMIQKVILHDVLKFLFVYIVFLLG
FGVALASLIEKCPKDNKDCSSYGSFSDAVLELFKLTIGLGDLNIQQNSKYPILFLFLLIT
YVILTFVLLLNMLIALMGETVENVSKESERIWRLQRARTILEFEKMLPEWLRSRFRMGEL
CKVAEDDFRLCLRINEVKWTEWKTHVSFLNEDPGPVRRTADFNKIQDSSRNNSKTTLNAF
EEVEEFPETSVLVPRGSAAAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
FZ4	2-aminoethyl diphenylborinate	C14 H16 B N O	8
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	32

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

Primary citation

TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site. Nadezhdin, K.D., Neuberger, A., Khosrof, L.S. et al. Sci Adv (2024) 10:eadn2453-eadn2453. DOI 10.1126/sciadv.adn2453 · 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
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
13LL 2.96 Å, Structure of human TRPV3-Q580P Olmsted syndrome mutant in the closed state

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