9KHK | pdb_00009khk

Cryo-EM structure of homomeric TRPC channel, class 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular architecture of the human TRPC1/C5 heteromeric channel.

Kim, S.H.Park, H.Kim, J.Kang, H.Won, J.Lee, B.C.So, I.Lee, H.H.

(2025) Nat Commun 17: 317-317

  • DOI: https://doi.org/10.1038/s41467-025-67024-9
  • Primary Citation of Related Structures:  
    9KHI, 9KHJ, 9KHK, 9LZY, 9LZZ

  • PubMed Abstract: 

    Transient receptor potential (TRP) ion channels form heteromers through combinatorial associations of distinct subunits, contributing to the diversity of TRP channel functions. Among them, TRPC5, which forms a heteromer with TRPC1, represents an attractive pharmaceutical target for treating anxiety and depression. Here, we present the cryo-electron microscopy structure of the human TRPC1/C5 heteromer, composed of one TRPC1 subunit and three TRPC5 subunits. The incorporation of TRPC1 into the heteromer disrupts the C 4 symmetry of the TRPC5 homotetramer, resulting in a distinct ion conduction pathway characterized by an asymmetrically constricted selectivity filter and an asymmetric lower gate. The TRPC1/C5 heteromer displays recognizable structural features compared to the TRPC1/C4 heteromer, including a noncanonically tilted coiled-coil domain and a distinct intersubunit interactions. Furthermore, we elucidate the structures of human TRPC5 bound to the TRPC1/4/5-specific agonist, (-)-Englerin A. Our findings establish a foundation for exploring the diversity of heteromeric TRP channels and pave the way for targeting TRPC1/C5 as a therapeutic strategy.


  • Organizational Affiliation
    • Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short transient receptor potential channel 5A,
B,
C [auth D],
D [auth C]
773Homo sapiensMutation(s): 0 
Gene Names: TRPC5TRP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL62 (Homo sapiens)
Explore Q9UL62 
Go to UniProtKB:  Q9UL62
PHAROS:  Q9UL62
GTEx:  ENSG00000072315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UL62
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
R [auth D],
Y [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
PTY
Query on PTY

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth D],
X [auth C]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
YZY (Subject of Investigation/LOI)
Query on YZY

Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
V [auth D],
W [auth C]
(2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
C37 H70 O5
DOZKMFVMCATMEH-OZKTZCCCSA-N
Y01 (Subject of Investigation/LOI)
Query on Y01

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
S [auth D],
Z [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C],
H [auth A],
O [auth B],
T [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
BA [auth C],
I [auth A],
P [auth B],
U [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Samsung Science and Technology FoundationKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references