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- PDB-9fxm: TRPC4 in complex with Z-AzPico -

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Basic information

Entry
Database: PDB / ID: 9fxm
TitleTRPC4 in complex with Z-AzPico
ComponentsTransient receptor potential cation channel subfamily c member 4a
KeywordsMEMBRANE PROTEIN / Transport Protein / Calcium channel
Function / homology
Function and homology information


monoatomic cation transport / monoatomic cation channel activity / calcium channel activity / plasma membrane
Similarity search - Function
Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Short transient receptor potential channel 4b
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVinayagam, D. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Chem Biol / Year: 2026
Title: Ideal efficacy photoswitching for chromocontrol of TRPC4/5 channel functions in live tissues.
Authors: Markus Müller / Konstantin Niemeyer / Navin K Ojha / Sebastian A Porav / Deivanayagabarathy Vinayagam / Nicole Urban / Fanny Büchau / Katharina Oleinikov / Mazen Makke / Claudia C Bauer / ...Authors: Markus Müller / Konstantin Niemeyer / Navin K Ojha / Sebastian A Porav / Deivanayagabarathy Vinayagam / Nicole Urban / Fanny Büchau / Katharina Oleinikov / Mazen Makke / Claudia C Bauer / Aidan V Johnson / Stephen P Muench / Frank Zufall / Dieter Bruns / Yvonne Schwarz / Stefan Raunser / Trese Leinders-Zufall / Robin S Bon / Michael Schaefer / Oliver Thorn-Seshold /
Abstract: Precisely probing the endogenous roles of target proteins is crucial for biological research. Photochemical tools can be photoactuated with high spatiotemporal resolution but often they are ...Precisely probing the endogenous roles of target proteins is crucial for biological research. Photochemical tools can be photoactuated with high spatiotemporal resolution but often they are unreliable in vivo because spatiotemporal variations of reagent concentration result in inhomogeneous bioactivity. We now describe ideal efficacy photoswitching, a paradigm that internally compensates for reagent concentration by self-competitive binding, allowing purely wavelength-dependent chromocontrol over bioactivity that is consistent from cell culture to deep tissues. We demonstrate this with photoswitches for endogenous transient receptor potential (TRP) C4 and C5 ion channels, reproducibly delivering strong agonism under 360-nm illumination, weak agonism under 385-nm illumination and strong antagonism under 440-nm illumination. These ligands unlock a range of high-precision investigations in TRP biology, from neuronal activity to exocytosis, reproductive signaling and smooth muscle contractility. The ideal efficacy photoswitching paradigm should also unlock high-performance chromocontrol over a wide range of sensory or signaling channels and receptors even in vivo.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily c member 4a
B: Transient receptor potential cation channel subfamily c member 4a
C: Transient receptor potential cation channel subfamily c member 4a
D: Transient receptor potential cation channel subfamily c member 4a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,6408
Polymers433,1244
Non-polymers2,5164
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transient receptor potential cation channel subfamily c member 4a / Transient receptor potential cation channel / subfamily C / member 4b


Mass: 108281.016 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpc4b, trpc4a / Plasmid: PEG-BacMAM / Organ (production host): embryonic KIDNEY / Production host: Homo sapiens (human) / Strain (production host): HEK293S / Variant (production host): GNTi- / References: UniProt: U3N7D8
#2: Chemical
ChemComp-A1IGY / (Z)-7-(4-chlorobenzyl)-1-(3-hydroxypropyl)-3-methyl-8-(4-(phenyldiazenyl)-3-(trifluoromethoxy)phenoxy)-3,7-dihydro-1H-purine-2,6-dione / 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-[4-[(~{Z})-phenyldiazenyl]-3-(trifluoromethyloxy)phenoxy]purine-2,6-dione


Mass: 628.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H24ClF3N6O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRPC4 -tetramer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.42 MDa / Experimental value: NO
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293S GNTI- / Plasmid: PEG BACMAM
Buffer solutionpH: 8.5
SpecimenConc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was homogenous
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 96 % / Chamber temperature: 277 K / Details: Vitrification done at liquid nitrogen temperature

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 490 nm / Calibrated defocus max: 3070 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 113 K / Temperature (min): 93 K
Image recordingAverage exposure time: 3.5 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3311 / Details: Images were collected in movie mode
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.7particle selection
2EPUimage acquisitionAFIS
4CTFFIND4CTF correction
7Coot9model fitting
9PHENIX1.21.1_5286:model refinement
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
12RELION3.1classification
13cryoSPARC43D reconstructionNon uniform refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 232983
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93651 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 57.21 / Protocol: OTHER / Space: REAL / Details: Phenix
Atomic model buildingPDB-ID: 6G1K

6g1k


Accession code: 6G1K / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221777
ELECTRON MICROSCOPYf_angle_d0.53629513
ELECTRON MICROSCOPYf_dihedral_angle_d13.6567879
ELECTRON MICROSCOPYf_chiral_restr0.0373295
ELECTRON MICROSCOPYf_plane_restr0.0043648

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