7D4P | pdb_00007d4p

Structure of human TRPC5 in complex with clemizole


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7D4P

This is version 1.2 of the entry. See complete history

Literature

Structural basis for human TRPC5 channel inhibition by two distinct inhibitors.

Song, K.Wei, M.Guo, W.Quan, L.Kang, Y.Wu, J.X.Chen, L.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.63429
  • Primary Citation Related Structures: 
    7D4P, 7D4Q, 7E4T

  • PubMed Abstract: 

    TRPC5 channel is a nonselective cation channel that participates in diverse physiological processes. TRPC5 inhibitors show promise in the treatment of anxiety disorder, depression, and kidney disease. However, the binding sites and inhibitory mechanism of TRPC5 inhibitors remain elusive. Here, we present the cryo-EM structures of human TRPC5 in complex with two distinct inhibitors, namely clemizole and HC-070, to the resolution of 2.7 Å. The structures reveal that clemizole binds inside the voltage sensor-like domain of each subunit. In contrast, HC-070 is wedged between adjacent subunits and replaces the glycerol group of a putative diacylglycerol molecule near the extracellular side. Moreover, we found mutations in the inhibitor binding pockets altered the potency of inhibitors. These structures suggest that both clemizole and HC-070 exert the inhibitory functions by stabilizing the ion channel in a nonconductive closed state. These results pave the way for further design and optimization of inhibitors targeting human TRPC5.


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

Macromolecule Content 

  • Total Structure Weight: 367.42 kDa 
  • Atom Count: 22,472 
  • Modeled Residue Count: 2,676 
  • Deposited Residue Count: 3,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Short transient receptor potential channel 5
A, B, C, D
764Homo sapiensMutation(s): 0 
Gene Names: TRPC5TRP5
Membrane Entity: Yes 
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 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV

Query on POV



Download:Ideal Coordinates CCD File
BA [auth D],
G [auth A],
N [auth B],
U [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
AA [auth D],
F [auth A],
M [auth B],
T [auth C]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
YZY

Query on YZY



Download:Ideal Coordinates CCD File
FA [auth D],
K [auth A],
R [auth B],
Y [auth C]
(2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
C37 H70 O5
DOZKMFVMCATMEH-OZKTZCCCSA-N
Y01

Query on Y01



Download:Ideal Coordinates CCD File
CA [auth D],
H [auth A],
O [auth B],
V [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
GX0
(Subject of Investigation/LOI)

Query on GX0



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
S [auth C],
Z [auth D]
1-[(4-chlorophenyl)methyl]-2-(pyrrolidin-1-ylmethyl)benzimidazole
C19 H20 Cl N3
CJXAEXPPLWQRFR-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
DA [auth D],
I [auth A],
P [auth B],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
EA [auth D],
J [auth A],
Q [auth B],
X [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GX0 BindingDB:  7D4P IC50: 1100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCV1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0502004
National Natural Science Foundation of China (NSFC)China31622021
National Science Foundation (NSF, China)China91857000
National Science Foundation (NSF, China)China31821091
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary