8GVX | pdb_00008gvx

Cryo-EM structure of the human TRPC5 ion channel in complex with G alpha i3 subunits, class2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8GVX

This is version 1.2 of the entry. See complete history

Literature

Molecular architecture of the G alpha i -bound TRPC5 ion channel.

Won, J.Kim, J.Jeong, H.Kim, J.Feng, S.Jeong, B.Kwak, M.Ko, J.Im, W.So, I.Lee, H.H.

(2023) Nat Commun 14: 2550-2550

  • DOI: https://doi.org/10.1038/s41467-023-38281-3
  • Primary Citation Related Structures: 
    7X6C, 7X6I, 8GVW, 8GVX

  • PubMed Abstract: 

    G-protein coupled receptors (GPCRs) and ion channels serve as key molecular switches through which extracellular stimuli are transformed into intracellular effects, and it has long been postulated that ion channels are direct effector molecules of the alpha subunit of G-proteins (Gα). However, no complete structural evidence supporting the direct interaction between Gα and ion channels is available. Here, we present the cryo-electron microscopy structures of the human transient receptor potential canonical 5 (TRPC5)-Gα i3 complexes with a 4:4 stoichiometry in lipid nanodiscs. Remarkably, Gα i3 binds to the ankyrin repeat edge of TRPC5 ~ 50 Å away from the cell membrane. Electrophysiological analysis shows that Gα i3 increases the sensitivity of TRPC5 to phosphatidylinositol 4,5-bisphosphate (PIP 2 ), thereby rendering TRPC5 more easily opened in the cell membrane, where the concentration of PIP 2 is physiologically regulated. Our results demonstrate that ion channels are one of the direct effector molecules of Gα proteins triggered by GPCR activation-providing a structural framework for unraveling the crosstalk between two major classes of transmembrane proteins: GPCRs and ion channels.


  • Organizational Affiliation
    • Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 535.18 kDa 
  • Atom Count: 32,872 
  • Modeled Residue Count: 3,964 
  • Deposited Residue Count: 4,532 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Short transient receptor potential channel 5A [auth B],
F [auth A],
G [auth C],
H [auth D]
773Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-3B [auth F],
C [auth E],
D [auth G],
E [auth H]
360Homo sapiensMutation(s): 1 
Gene Names: GNAI3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P08754 (Homo sapiens)
Explore P08754 
Go to UniProtKB:  P08754
PHAROS:  P08754
GTEx:  ENSG00000065135 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08754
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTY
(Subject of Investigation/LOI)

Query on PTY



Download:Ideal Coordinates CCD File
BA [auth D],
I [auth B],
R [auth A],
W [auth C]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
YZY
(Subject of Investigation/LOI)

Query on YZY



Download:Ideal Coordinates CCD File
AA [auth C],
FA [auth D],
M [auth B],
V [auth A]
(2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
C37 H70 O5
DOZKMFVMCATMEH-OZKTZCCCSA-N
GTP
(Subject of Investigation/LOI)

Query on GTP



Download:Ideal Coordinates CCD File
N [auth F],
O [auth E],
P [auth G],
Q [auth H]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Y01
(Subject of Investigation/LOI)

Query on Y01



Download:Ideal Coordinates CCD File
CA [auth D],
J [auth B],
S [auth A],
X [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
DA [auth D],
K [auth B],
T [auth A],
Y [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
EA [auth D],
L [auth B],
U [auth A],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.91 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
Other privateKorea, Republic OfSSTF-BA2101-13

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection