8GKA: PDB entry 8GKA

Human TRPV3 tetramer structure, closed conformation. Determined by electron microscopy at 2.55 Å resolution. Released 6 Sept 2023.

Method: Electron microscopy
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 21,812
Mol. weight: 388.08 kDa
Ligands: POV
Released: 6 Sept 2023

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

Secondary structure: helices and β-sheets

8GKA contains 132 α-helices and 52 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: 33 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	119-129	11
α-helix	135-147	13
α-helix	154-162	9
β-strand	163	1	1
β-strand	170	1	1
α-helix	171-177	7
α-helix	183-196	14
α-helix	200-204	5
β-strand	207	1	2
β-strand	208	1	3
β-strand	214	1	3
β-strand	217	1	2
α-helix	218-224	7
α-helix	228-237	10
α-helix	265-271	7
α-helix	275-283	9
α-helix	299-306	8
α-helix	316-328	13
α-helix	344-351	8
α-helix	354-361	8
β-strand	376-382	7	4
β-strand	385-391	7	4
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	484-508	25
α-helix	513-519	7
α-helix	521-541	21
α-helix	547-560	14
α-helix	561-566	6
α-helix	570-582	13
α-helix	583-587	5
α-helix	588-607	20
β-strand	609	1	5
α-helix	610-613	4
α-helix	625-636	12
β-strand	648	1	5
α-helix	651-662	12
α-helix	663-669	7
α-helix	670-685	16
α-helix	688-706	19
β-strand	719-723	5	6
β-strand	727-730	4	6
β-strand	731-737	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 3	A, B, C, D	protein	790	Homo sapiens	Q8NET8 (AlphaFold model)

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

>8GKA_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
CKVAEDDFRLCLRINEVKWTEWKTHVSFLNEDPGPVRRTDFNKIQDSSRNNSKTTLNAFE
EVEEFPETSV

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	33

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

Primary citation

A pentameric TRPV3 channel with a dilated pore. Lansky, S., Betancourt, J.M., Zhang, J. et al. Nature (2023) 621:206-214. DOI 10.1038/s41586-023-06470-1 · 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
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
13LL 2.96 Å, Structure of human TRPV3-Q580P Olmsted syndrome mutant in the closed state

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