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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


store-operated calcium channel activity / inositol 1,4,5 trisphosphate binding / cation channel complex / monoatomic cation transport / regulation of cytosolic calcium ion concentration / monoatomic cation channel activity / calcium ion transmembrane transport / 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: To Be Published
Title: TRPC4 in complex with Z-AzPico
Authors: Vinayagam, D. / Raunser, S.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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