8FFN: RR-bound wildtype rabbit TRPV5 in nanodiscs

RR-bound wildtype rabbit TRPV5 in nanodiscs. Determined by electron microscopy at 2.96 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 2.96 Å
Organism: Oryctolagus cuniculus
Chains: 4
Atoms: 19,871
Mol. weight: 344.97 kDa
Ligands: R2R, POV, ERG
Released: 7 Feb 2024

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

Secondary structure: helices and β-sheets

8FFN contains 152 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: 38 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-54	7
α-helix	58-66	9
α-helix	82-88	7
α-helix	92-101	10
α-helix	103-106	4
α-helix	113-115	3
α-helix	120-126	7
α-helix	130-139	10
α-helix	166-173	8
α-helix	176-184	9
α-helix	199-204	6
α-helix	211-221	11
α-helix	232-234	3
α-helix	235-237	3
α-helix	243-250	8
α-helix	253-259	7
β-strand	266-270	5	1
β-strand	273-279	7	1
α-helix	281-284	4
α-helix	292-297	6
α-helix	302-309	8
α-helix	313-320	8
α-helix	321-325	5
α-helix	326-348	23
β-strand	352-354	3	2
β-strand	366	1	3
β-strand	368-370	3	2
α-helix	373-376	4
α-helix	380-410	31
α-helix	412-417	6
α-helix	423-445	23
α-helix	451-463	13
α-helix	464-471	8
α-helix	476-486	11
α-helix	489-511	23
β-strand	515	1	4
α-helix	526-537	12
α-helix	553-562	10
α-helix	563-570	8
α-helix	571-584	14
α-helix	586-607	22
α-helix	610-612	3
α-helix	614-616	3
β-strand	618-619	2	1
β-strand	629-636	8	1

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

>8FFN_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
R2R	ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)	H42 N14 O2 Ru3	1
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	8
ERG	Ergosterol	C28 H44 O	8

Primary citation

Molecular details of ruthenium red pore block in TRPV channels. Pumroy, R.A., De Jesus-Perez, J.J., Protopopova, A.D. et al. EMBO Rep (2024) 25:506-523. DOI 10.1038/s44319-023-00050-0 · 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
8TF3 2.94 Å, Wildtype rabbit TRPV5 into nanodiscs in complex with econazole
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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