6O20: TRPV5 with calmodulin bound

Cryo-EM structure of TRPV5 with calmodulin bound. Determined by electron microscopy at 3.3 Å resolution. Released 24 Apr 2019.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Oryctolagus cuniculus, Bos taurus
Chains: 6
Atoms: 20,950
Mol. weight: 433.68 kDa
Ligands: CA
Released: 24 Apr 2019

Explore 6O20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O20 contains 159 α-helices and 42 β-strands across 6 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: 38 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-55	8
α-helix	58-61	4
α-helix	82-88	7
α-helix	92-100	9
α-helix	103-105	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-171	6
α-helix	176-183	8
α-helix	199-202	4
α-helix	209-219	11
α-helix	223-224	2
α-helix	232-234	3
α-helix	243-250	8
α-helix	253-259	7
α-helix	260-263	4
β-strand	264	1	1
β-strand	268	1	1
β-strand	273-278	6	1
α-helix	281-284	4
α-helix	292-297	6
α-helix	302-309	8
α-helix	314-320	7
α-helix	321-325	5
α-helix	327-348	22
β-strand	354	1	2
β-strand	368	1	3
β-strand	370	1	2
α-helix	383-402	20
α-helix	405-408	4
α-helix	426-442	17
α-helix	451-461	11
α-helix	462-471	10
α-helix	476-486	11
α-helix	490-511	22
β-strand	515	1	4
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	1
α-helix	642-652	11

Chains B, C and D: 37 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	29-46	18
α-helix	48-55	8
α-helix	58-61	4
α-helix	82-88	7
α-helix	92-100	9
α-helix	103-105	3
α-helix	120-126	7
α-helix	130-138	9
α-helix	166-171	6
α-helix	176-183	8
α-helix	199-202	4
α-helix	209-219	11
α-helix	223-224	2
α-helix	232-234	3
α-helix	243-250	8
α-helix	253-259	7
α-helix	260-263	4
β-strand	264	1	7
β-strand	268	1	7
β-strand	273-278	6	7
α-helix	281-284	4
α-helix	292-297	6
α-helix	302-309	8
α-helix	314-320	7
α-helix	321-325	5
α-helix	327-348	22
β-strand	354	1	8
β-strand	368	1	9
β-strand	370	1	8
α-helix	383-402	20
α-helix	405-408	4
α-helix	426-442	17
α-helix	451-461	11
α-helix	462-471	10
α-helix	476-486	11
α-helix	490-511	22
β-strand	515	1	3
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	10
β-strand	629-630	2	10
β-strand	631-636	6	7

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	699-709	11

Chain F: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	27	1	6
α-helix	31-38	8
α-helix	43-44	2
α-helix	48-52	5
β-strand	63	1	6
α-helix	65-74	10
α-helix	85-92	8
α-helix	106-112	7
α-helix	118-128	11
α-helix	138-143	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transient receptor potential cation channel subfamily V member 5	A, B, C, D, E	protein	730	Oryctolagus cuniculus	Q9XSM3 (AlphaFold model)
Calmodulin	F	protein	169	Bos taurus	P62157 (AlphaFold model)

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

>6O20_1 Transient receptor potential cation channel subfamily V member 5 (chains A, B, C, D, E)
MGACPPKAKGPWAQLQKLLISWPVGEQDWEQYRDRVNMLQQERIRDSPLLQAAKENDLRL
LKILLLNQSCDFQQRGAVGETALHVAALYDNLEAATLLMEAAPELAKEPALCEPFVGQTA
LHIAVMNQNLNLVRALLARGASVSARATGAAFRRSPHNLIYYGEHPLSFAACVGSEEIVR
LLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDEHSDHLQSLELVPNHQG
LTPFKLAGVEGNTVMFQHLMQKRKHVQWTCGPLTSTLYDLTEIDSWGEELSFLELVVSSK
KREARQILEQTPVKELVSFKWKKYGRPYFCVLASLYILYMICFTTCCIYRPLKLRDDNRT
DPRDITILQQKLLQEAYVTHQDNIRLVGELVTVTGAVIILLLEIPDIFRVGASRYFGQTI
LGGPFHVIIITYASLVLLTMVMRLTNMNGEVVPLSFALVLGWCSVMYFARGFQMLGPFTI
MIQKMIFGDLMRFCWLMAVVILGFASAFHITFQTEDPNNLGEFSDYPTALFSTFELFLTI
IDGPANYSVDLPFMYCITYAAFAIIATLLMLNLFIAMMGDTHWRVAQERDELWRAQVVAT
TVMLERKMPRFLWPRSGICGYEYGLGDRWFLRVENHHDQNPLRVLRYVEAFKCSDKEDGQ
EQLSEKRPSTVESGMLSRASVAFQTPSLSRTTSQSSNSHRGWEILRRNTLGHLNLGLDLG
EGDGEEVYHF

Sequence of entity 2 (F), FASTA

>6O20_2 Calmodulin (chains F)
MGSSHHHHHHSSGLVPRGSHMADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSL
GQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGY
ISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

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
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
8FFN 2.96 Å, RR-bound wildtype rabbit TRPV5 in nanodiscs
6O1P 3.0 Å, Cryo-EM structure of full length TRPV5 in nanodisc

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