6G1K | pdb_00006g1k

Electron cryo-microscopy structure of the canonical TRPC4 ion channel


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6G1K

This is version 1.3 of the entry. See complete history

Literature

Electron cryo-microscopy structure of the canonical TRPC4 ion channel.

Vinayagam, D.Mager, T.Apelbaum, A.Bothe, A.Merino, F.Hofnagel, O.Gatsogiannis, C.Raunser, S.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.36615
  • Primary Citation Related Structures: 
    6G1K

  • PubMed Abstract: 

    Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca 2+ signaling and have been proposed to act as store-operated channels (SOC). Their malfunction is related to cardiomyopathies and their modulation by small molecules has been shown to be effective against renal cancer cells. The molecular mechanism underlying the complex activation and regulation is poorly understood. Here, we report the electron cryo-microscopy structure of zebrafish TRPC4 in its unliganded (apo), closed state at an overall resolution of 3.6 Å. The structure reveals the molecular architecture of the cation conducting pore, including the selectivity filter and lower gate. The cytoplasmic domain contains two key hubs that have been shown to interact with modulating proteins. Structural comparisons with other TRP channels give novel insights into the general architecture and domain organization of this superfamily of channels and help to understand their function and pharmacology.


  • Organizational Affiliation
    • Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 427.16 kDa 
  • Atom Count: 21,428 
  • Modeled Residue Count: 2,592 
  • Deposited Residue Count: 3,684 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily c member 4a
A, B, C, D
921Danio rerioMutation(s): 0 
Gene Names: trpc4btrpc4a
Membrane Entity: Yes 
UniProt
Find proteins for U3N7D8 (Danio rerio)
Explore U3N7D8 
Go to UniProtKB:  U3N7D8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU3N7D8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
44E

Query on 44E



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
C15 H29 O8 P
SFZZRGHNPILUOD-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPHIRE1.0
MODEL REFINEMENTPHENIX1.13

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany615984
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2018-08-01
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary