9KDB: HTRPC3

Structure of hTRPC3 in complex with Nb1-25 at 2.67 angstrom. Determined by electron microscopy at 2.67 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 2.67 Å
Organisms: Camelus, Homo sapiens
Chains: 8
Atoms: 27,596
Mol. weight: 507.56 kDa
Ligands: A1L5I, CA, ZN
Released: 8 Oct 2025

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

Secondary structure: helices and β-sheets

9KDB contains 192 α-helices and 76 β-strands across 8 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: 45 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	26-36	11
α-helix	40-49	10
α-helix	65-71	7
α-helix	75-83	9
α-helix	90-100	11
α-helix	103-109	7
α-helix	113-116	4
α-helix	125-131	7
β-strand	137	1	4
β-strand	143	1	4
α-helix	151-158	8
α-helix	161-169	9
α-helix	174-176	3
α-helix	185-193	9
α-helix	197-209	13
α-helix	212-218	7
α-helix	222-239	18
α-helix	244-263	20
α-helix	268-276	9
α-helix	295-302	8
α-helix	306-310	5
α-helix	312-322	11
α-helix	327-330	4
α-helix	334-346	13
α-helix	348-357	10
α-helix	362-367	6
α-helix	370-391	22
α-helix	393-395	3
α-helix	415-420	6
α-helix	424-446	23
α-helix	456-492	37
α-helix	505-508	4
α-helix	509-511	3
α-helix	514-516	3
α-helix	522-538	17
α-helix	539-543	5
α-helix	545-547	3
α-helix	552-587	36
β-strand	594	1	5
α-helix	602-611	10
α-helix	612-614	3
α-helix	619-622	4
β-strand	624	1	5
α-helix	629-662	34
α-helix	669-685	17
α-helix	693-695	3
α-helix	762-782	21
β-strand	786	1	6
α-helix	787	1
β-strand	788	1	7
α-helix	789-823	35

Chains E, F, G and H: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-13	3	2
β-strand	17-25	9	1
β-strand	31-37	7	3
β-strand	44-49	6	3
β-strand	55-57	3	3
β-strand	63	1	1
β-strand	66-70	5	1
β-strand	76-82	7	1
α-helix	86-88	3
β-strand	90-97	8	3
α-helix	104-106	3
α-helix	109-111	3
β-strand	114-115	2	3
β-strand	119-121	3	3
β-strand	122-124	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nb1-25	E, F, G, H	protein	184	Camelus
Short transient receptor potential channel 3	A, B, C, D	protein	921	Homo sapiens	Q13507 (AlphaFold model)

Sequence of entity 1 (E, F, G, H), FASTA

>9KDB_1 Nb1-25 (chains E, F, G, H)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGSVQSGGSLRLSCAASGDKNYYMGWFRQA
PGKEREGVAAIKSDGETRYADSSVTGRFTISQDNAKKTLYLQMTSLKPEDTAMYYCAADR
YIGTRWKYVRPEDYSYWGQGTQVTVSSAAAYPYDVPDYALEGSGPSRLEEELRRRLTEHH
HHHH

Sequence of entity 2 (A, B, C, D), FASTA

>9KDB_2 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
A1L5I	[(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate	C39 H72 O5	4
CA	Calcium ion	Ca	12
ZN	Zinc ion	Zn	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)
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
9OLX 3.3 Å, Structure of a constitutively open human TRPC3 mutant in the inhibited state

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