6O1N: TRPV5 (1-660) in nanodisc

Cryo-EM structure of TRPV5 (1-660) in nanodisc. Determined by electron microscopy at 2.9 Å resolution. Released 24 Apr 2019.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Oryctolagus cuniculus
Chains: 4
Atoms: 19,608
Mol. weight: 331.6 kDa
Released: 24 Apr 2019

Explore 6O1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O1N contains 164 α-helices and 24 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.

Chain A: 41 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-54	7
α-helix	58-63	6
α-helix	82-88	7
α-helix	92-101	10
α-helix	113-115	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-172	7
α-helix	176-183	8
α-helix	199-204	6
α-helix	209-211	3
α-helix	213-221	9
α-helix	232-234	3
α-helix	243-249	7
α-helix	253-258	6
α-helix	261-263	3
β-strand	264-268	5	1
β-strand	273-278	6	1
α-helix	292-297	6
α-helix	302-309	8
α-helix	320	1
α-helix	321-325	5
α-helix	328-331	4
α-helix	337-343	7
α-helix	344-346	3
α-helix	390-393	4
α-helix	398-401	4
α-helix	404-406	3
α-helix	407-410	4
α-helix	428-442	15
α-helix	451-461	11
α-helix	462-468	7
α-helix	478-487	10
α-helix	500-503	4
α-helix	505-511	7
α-helix	526-537	12
α-helix	542-543	2
β-strand	550	1	2
α-helix	553-564	12
α-helix	565-570	6
α-helix	571-580	10
α-helix	590-607	18
α-helix	614-615	2
β-strand	618-619	2	3
β-strand	629-630	2	3
β-strand	631-636	6	1

Chain B: 41 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-54	7
α-helix	58-63	6
α-helix	82-88	7
α-helix	92-101	10
α-helix	113-115	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-172	7
α-helix	176-183	8
α-helix	199-204	6
α-helix	209-211	3
α-helix	213-221	9
α-helix	232-234	3
α-helix	243-249	7
α-helix	253-258	6
α-helix	261-263	3
β-strand	264-268	5	4
β-strand	273-278	6	4
α-helix	292-297	6
α-helix	302-309	8
α-helix	320	1
α-helix	321-325	5
α-helix	328-331	4
α-helix	337-343	7
α-helix	344-346	3
α-helix	390-393	4
α-helix	398-401	4
α-helix	404-406	3
α-helix	407-410	4
α-helix	428-442	15
α-helix	451-461	11
α-helix	462-468	7
α-helix	478-487	10
α-helix	500-503	4
α-helix	505-511	7
α-helix	526-537	12
α-helix	542-543	2
α-helix	553-564	12
α-helix	565-570	6
α-helix	571-580	10
α-helix	590-607	18
α-helix	614-615	2
β-strand	618-619	2	5
β-strand	629-630	2	5
β-strand	631-636	6	4

Chain C: 41 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-54	7
α-helix	58-63	6
α-helix	82-88	7
α-helix	92-101	10
α-helix	113-115	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-172	7
α-helix	176-183	8
α-helix	199-204	6
α-helix	209-211	3
α-helix	213-221	9
α-helix	232-234	3
α-helix	243-249	7
α-helix	253-258	6
α-helix	261-263	3
β-strand	264-268	5	6
β-strand	273-278	6	6
α-helix	292-297	6
α-helix	302-309	8
α-helix	320	1
α-helix	321-325	5
α-helix	328-331	4
α-helix	337-343	7
α-helix	344-346	3
β-strand	366	1	7
α-helix	390-393	4
α-helix	398-401	4
α-helix	404-406	3
α-helix	407-410	4
α-helix	428-442	15
α-helix	451-461	11
α-helix	462-468	7
α-helix	478-487	10
α-helix	500-503	4
α-helix	505-511	7
α-helix	526-537	12
α-helix	542-543	2
α-helix	553-564	12
α-helix	565-570	6
α-helix	571-580	10
α-helix	590-607	18
α-helix	614-615	2
β-strand	618-619	2	8
β-strand	629-630	2	8
β-strand	631-636	6	6

Chain D: 41 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-54	7
α-helix	58-63	6
α-helix	82-88	7
α-helix	92-101	10
α-helix	113-115	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-172	7
α-helix	176-183	8
α-helix	199-204	6
α-helix	209-211	3
α-helix	213-221	9
α-helix	232-234	3
α-helix	243-249	7
α-helix	253-258	6
α-helix	261-263	3
β-strand	264-268	5	9
β-strand	273-278	6	9
α-helix	292-297	6
α-helix	302-309	8
α-helix	320	1
α-helix	321-325	5
α-helix	328-331	4
α-helix	337-343	7
α-helix	344-346	3
β-strand	366	1	2
α-helix	390-393	4
α-helix	398-401	4
α-helix	404-406	3
α-helix	407-410	4
α-helix	428-442	15
α-helix	451-461	11
α-helix	462-468	7
α-helix	478-487	10
α-helix	500-503	4
α-helix	505-511	7
α-helix	526-537	12
α-helix	542-543	2
β-strand	550	1	7
α-helix	553-564	12
α-helix	565-570	6
α-helix	571-580	10
α-helix	590-607	18
α-helix	614-615	2
β-strand	618-619	2	10
β-strand	629-630	2	10
β-strand	631-636	6	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 5	A, B, C, D	protein	730	Oryctolagus cuniculus	Q9XSM3 (AlphaFold model)

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

>6O1N_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
EGDGEEVYHF

Primary citation

Structural insight into TRPV5 channel function and modulation. Dang, S., van Goor, M.K., Asarnow, D. et al. Proc Natl Acad Sci U S A (2019) 116:8869-8878. DOI 10.1073/pnas.1820323116 · 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
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
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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