9KDB | pdb_00009kdb

Structure of hTRPC3 in complex with Nb1-25 at 2.67 angstrom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 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

Structural mechanism of the agonist binding on human TRPC3 channel.

Chen, Y.Zang, J.Guo, W.Xu, J.Wei, M.Quan, L.Zhu, M.Zhao, X.Peng, H.Wan, Y.Chen, L.

(2025) Nat Commun 16: 9343-9343

  • DOI: https://doi.org/10.1038/s41467-025-64435-6
  • Primary Citation of Related Structures:  
    9KDB, 9KDC, 9KDD, 9KDE, 9U5C

  • PubMed Abstract: 

    TRPC3/6/7 channels are cation channels that are directly activated by the second messenger diacylglycerol (DAG). These channels play crucial physiological roles and are implicated in various disease conditions; however, the binding mechanism of DAG to these channels remains incompletely understood. In this study, we present the structures of human TRPC3 in complex with DAG or synthetic activators, 4n and GSK1702934A. The structural analysis reveals that DAG binds at the L2 site, located near the pore on the extracellular side of TRPC3. Functional assays confirmed that the L2 site serves as the activating site for DAG. Notably, both 4n and GSK1702934A competitively bind to the same site, facilitating channel activation. Moreover, based on the pharmacophore identified from the DAG-bound structure, we found that monoacylglycerols (MAGs) are endogenous activators of TRPC3/6/7 channels, providing new insights into their regulatory mechanisms.


  • Organizational Affiliation
    • State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nb1-25A [auth E],
C [auth F],
E [auth G],
G [auth H]
184CamelusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Short transient receptor potential channel 3B [auth A],
D [auth B],
F [auth C],
H [auth D]
921Homo sapiensMutation(s): 0 
Gene Names: TRPC3TRP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13507 (Homo sapiens)
Explore Q13507 
Go to UniProtKB:  Q13507
PHAROS:  Q13507
GTEx:  ENSG00000138741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13507
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L5I (Subject of Investigation/LOI)
Query on A1L5I

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
S [auth B],
X [auth C]
[(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
C39 H72 O5
AFSHUZFNMVJNKX-SKNMGDSLSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B],
T [auth C],
Y [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
J [auth A]
K [auth A]
L [auth A]
AA [auth D],
BA [auth D],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFA1303000
National Natural Science Foundation of China (NSFC)China32225027

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references