8TF3: Wildtype rabbit TRPV5 into nanodiscs

Wildtype rabbit TRPV5 into nanodiscs in complex with econazole. Determined by electron microscopy at 2.94 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.94 Å
Organism: Oryctolagus cuniculus
Chains: 4
Atoms: 19,888
Mol. weight: 345.9 kDa
Ligands: CPL, ECN, ERG
Released: 10 Jan 2024

Explore 8TF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TF3 contains 168 α-helices and 56 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: 42 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-55	8
α-helix	58-66	9
β-strand	75	1	1
β-strand	81	1	1
α-helix	82-88	7
α-helix	92-101	10
α-helix	103-107	5
α-helix	108	1
β-strand	109	1	2
α-helix	110	1
β-strand	119	1	2
α-helix	120-126	7
α-helix	130-137	8
α-helix	150-152	3
α-helix	166-173	8
α-helix	176-184	9
α-helix	199-204	6
α-helix	209-220	12
α-helix	232-234	3
α-helix	243-249	7
α-helix	253-260	8
β-strand	264-270	7	3
β-strand	273-279	7	3
α-helix	281-284	4
α-helix	292-297	6
α-helix	304-309	6
α-helix	311-320	10
α-helix	321-325	5
α-helix	326-348	23
β-strand	352-354	3	4
β-strand	364	1	5
β-strand	366	1	6
β-strand	368-370	3	4
α-helix	371-372	2
α-helix	380-410	31
α-helix	412-417	6
α-helix	423-444	22
α-helix	451-463	13
α-helix	464-471	8
α-helix	476-485	10
α-helix	486-490	5
α-helix	491-512	22
β-strand	515	1	7
α-helix	521-523	3
α-helix	526-537	12
α-helix	542-544	3
β-strand	550	1	8
α-helix	553-562	10
α-helix	563-571	9
α-helix	572-607	36
α-helix	610-612	3
α-helix	614-616	3
β-strand	618-619	2	3
α-helix	621-623	3
β-strand	629-636	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 5	A, B, C, D	protein	739	Oryctolagus cuniculus	Q9XSM3 (AlphaFold model)

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

>8TF3_1 Transient receptor potential cation channel subfamily V member 5 (chains A, B, C, D)
MGACPPKAKGPWAQLQKLLISWPVGEQDWEQYRDRVNMLQQERIRDSPLLQAAKENDLRL
LKILLLNQSCDFQQRGAVGETALHVAALYDNLEAATLLMEAAPELAKEPALCEPFVGQTA
LHIAVMNQNLNLVRALLARGASVSARATGAAFRRSPHNLIYYGEHPLSFAACVGSEEIVR
LLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDEHSDHLQSLELVPNHQG
LTPFKLAGVEGNTVMFQHLMQKRKHVQWTCGPLTSTLYDLTEIDSWGEELSFLELVVSSK
KREARQILEQTPVKELVSFKWKKYGRPYFCVLASLYILYMICFTTCCIYRPLKLRDDNRT
DPRDITILQQKLLQEAYVTHQDNIRLVGELVTVTGAVIILLLEIPDIFRVGASRYFGQTI
LGGPFHVIIITYASLVLLTMVMRLTNMNGEVVPLSFALVLGWCSVMYFARGFQMLGPFTI
MIQKMIFGDLMRFCWLMAVVILGFASAFHITFQTEDPNNLGEFSDYPTALFSTFELFLTI
IDGPANYSVDLPFMYCITYAAFAIIATLLMLNLFIAMMGDTHWRVAQERDELWRAQVVAT
TVMLERKMPRFLWPRSGICGYEYGLGDRWFLRVENHHDQNPLRVLRYVEAFKCSDKEDGQ
EQLSEKRPSTVESGMLSRASVAFQTPSLSRTTSQSSNSHRGWEILRRNTLGHLNLGLDLG
EGDGEEVYHFTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
CPL	1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine	C42 H80 N O8 P	8
ECN	1-[(2S)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole	C18 H15 Cl3 N2 O	4
ERG	Ergosterol	C28 H44 O	8

Primary citation

Structural mechanism of TRPV5 inhibition by econazole. De Jesus-Perez, J.J., Gabrielle, M., Raheem, S. et al. Structure (2024) 32:148-156.e5. DOI 10.1016/j.str.2023.11.012 · PubMed

Other PDB entries of the same protein (UniProt Q9XSM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8TF2 2.57 Å, Wildtype rabbit TRPV5 into nanodiscs in Apo state
7T6O 2.6 Å, Cryo-EM structure of TRPV5 in nanodiscs at pH6 state 3
8FFQ 2.65 Å, Wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and ruthenium red
6O1U 2.8 Å, Cryo-EM structure of TRPV5 W583A in nanodisc
7T6M 2.8 Å, Cryo-EM structure of TRPV5 in nanodiscs with PI(4,5)P2 at pH6 state 1
7T6P 2.8 Å, Cryo-EM structure of TRPV5 T709D in nanodiscs
8TF4 2.86 Å, Wildtype rabbit TRPV5 into nanodiscs in the presence of PI(4,5)P2 and econazole
6O1N 2.9 Å, Cryo-EM structure of TRPV5 (1-660) in nanodisc
7T6N 2.9 Å, Cryo-EM structure of TRPV5 in nanodiscs at pH6 state 2
8FFN 2.96 Å, RR-bound wildtype rabbit TRPV5 in nanodiscs
6O1P 3.0 Å, Cryo-EM structure of full length TRPV5 in nanodisc
7T6K 3.0 Å, Cryo-EM structure of TRPV5 at pH6 in nanodiscs

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