9KDE: 4n-bound TRPC3

Structure of 4n-bound TRPC3 at 3.3 angstrom. Determined by electron microscopy at 3.34 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 3.34 Å
Organism: Homo sapiens
Chains: 4
Atoms: 21,968
Mol. weight: 424.71 kDa
Ligands: ZN, A1L5Q
Released: 8 Oct 2025

Explore 9KDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KDE contains 164 α-helices and 16 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: 41 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-36	11
α-helix	40-46	7
α-helix	65-71	7
α-helix	75-82	8
α-helix	90-99	10
α-helix	103-110	8
α-helix	113-116	4
β-strand	137	1	1
β-strand	143	1	1
α-helix	151-158	8
α-helix	161-169	9
α-helix	175-179	5
α-helix	185-192	8
α-helix	195-210	16
α-helix	212-218	7
α-helix	222-240	19
α-helix	244-263	20
α-helix	268-275	8
α-helix	295-302	8
α-helix	306-309	4
α-helix	312-322	11
α-helix	334-346	13
α-helix	348-354	7
α-helix	358-360	3
α-helix	362-367	6
α-helix	370-391	22
α-helix	415-420	6
α-helix	422-423	2
α-helix	424-447	24
α-helix	449-454	6
α-helix	456-491	36
α-helix	505-508	4
α-helix	509-511	3
α-helix	514-516	3
α-helix	522-537	16
α-helix	538-543	6
α-helix	545-547	3
α-helix	552-587	36
β-strand	594	1	2
α-helix	602-611	10
α-helix	619-622	4
β-strand	624	1	2
α-helix	629-659	31
α-helix	668-685	18
α-helix	762-784	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Short transient receptor potential channel 3	A, B, C, D	protein	921	Homo sapiens	Q13507 (AlphaFold model)

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

>9KDE_1 Short transient receptor potential channel 3 (chains A, B, C, D)
MSTKVRKCKEQARVTFPAPEEEEDEGEDEGAEPQRRRRGWRGVNGGLEPRSAPSQREPHG
YCPPPFSHGPDLSMEGSPSLRRMTVMREKGRRQAVRGPAFMFNDRGTSLTAEEERFLDAA
EYGNIPVVRKMLEESKTLNVNCVDYMGQNALQLAVGNEHLEVTELLLKKENLARIGDALL
LAISKGYVRIVEAILNHPGFAASKRLTLSPCEQELQDDDFYAYDEDGTRFSPDITPIILA
AHCQKYEVVHMLLMKGARIERPHDYFCKCGDCMEKQRHDSFSHSRSRINAYKGLASPAYL
SLSSEDPVLTALELSNELAKLANIEKEFKNDYRKLSMQCKDFVVGVLDLCRDSEEVEAIL
NGDLESAEPLEVHRHKASLSRVKLAIKYEVKKFVAHPNCQQQLLTIWYENLSGLREQTIA
IKCLVVLVVALGLPFLAIGYWIAPCSRLGKILRSPFMKFVAHAASFIIFLGLLVFNASDR
FEGITTLPNITVTDYPKQIFRVKTTQFTWTEMLIMVWVLGMMWSECKELWLEGPREYILQ
LWNVLDFGMLSIFIAAFTARFLAFLQATKAQQYVDSYVQESDLSEVTLPPEIQYFTYARD
KWLPSDPQIISEGLYAIAVVLSFSRIAYILPANESFGPLQISLGRTVKDIFKFMVLFIMV
FFAFMIGMFILYSYYLGAKVNAAFTTVEESFKTLFWSIFGLSEVTSVVLKYDHKFIENIG
YVLYGIYNVTMVVVLLNMLIAMINSSYQEIEDDSDVEWKFARSKLWLSYFDDGKTLPPPF
SLVPSPKSFVYFIMRIVNFPKCRRRRLQKDIEMGMGNSKSRLNLFTQSNSRVFESHSFNS
ILNQPTRYQQIMKRLIKRYVLKAQVDKENDEVNEGELKEIKQDISSLRYELLEDKSQATE
ELAILIHKLSEKLNPSMLRCE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
A1L5Q	ethyl 4-[2-methyl-7-oxidanyl-3-[4-(trifluoromethyl)phenyl]pyrazolo[1,5-a]pyrimi…	C22 H23 F3 N4 O3	4

Primary citation

Structural mechanism of the agonist binding on human TRPC3 channel. Chen, Y., Zang, J., Guo, W. et al. Nat Commun (2025) 16:9343-9343. DOI 10.1038/s41467-025-64435-6 · PubMed

Other PDB entries of the same protein (UniProt Q13507 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U5C 2.25 Å, Structure of hTRPC3 in complex with Nb1-94 at 2.25 angstrom
9OLM 2.5 Å, Structure of human TRPC3 cerebellar splice variant (isoform c)
9KDB 2.67 Å, Structure of hTRPC3 in complex with Nb1-25 at 2.67 angstrom
7DXB 2.7 Å, Structure of TRPC3 at 2.7 angstrom in high calcium state
9KDD 2.7 Å, Structure of GSK1702934A-bound TRPC3 at 3.3 angstrom
9VFI 2.72 Å, Structure of hTRPC3 solubilized with 4F peptide at 2.72 angstrom
9OLK 2.8 Å, Structure of wild-type human TRPC3
9KDC 3.01 Å, Structure of hTRPC3 in complex with Nb3-37 at 3.01 angstrom
7DXC 3.06 Å, Structure of TRPC3 at 3.06 angstrom in low calcium state
9OLL 3.1 Å, Structure of human TRPC3 T573A mutant
7DXE 3.2 Å, Structure of TRPC3 gain of function mutation R803C at 3.2 angstrom in 1340nM free…
6CUD 3.3 Å, Structure of the human TRPC3 in a lipid-occupied, closed state

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