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- EMDB-50851: TRPC4 in complex with Z-AzPico -

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Basic information

Entry
Database: EMDB / ID: EMD-50851
TitleTRPC4 in complex with Z-AzPico
Map dataPost processed map
Sample
  • Organelle or cellular component: TRPC4 -tetramer
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: (Z)-7-(4-chlorobenzyl)-1-(3-hydroxypropyl)-3-methyl-8-(4-(phenyldiazenyl)-3-(trifluoromethoxy)phenoxy)-3,7-dihydro-1H-purine-2,6-dione
KeywordsTransport Protein / Calcium channel / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVinayagam D / Raunser S
Funding support Germany, 1 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50851.png

Downloads & links

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Map

FileDownload / File: emd_50851.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å		0.91 Å/pix.
x 300 pix.
= 273. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-2.4760473 - 3.9856868
Average (Standard dev.)0.004764794 (±0.10218967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 273.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50851_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50851_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPC4 -tetramer

EntireName: TRPC4 -tetramer
Components
  • Organelle or cellular component: TRPC4 -tetramer
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: (Z)-7-(4-chlorobenzyl)-1-(3-hydroxypropyl)-3-methyl-8-(4-(phenyldiazenyl)-3-(trifluoromethoxy)phenoxy)-3,7-dihydro-1H-purine-2,6-dione

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Supramolecule #1: TRPC4 -tetramer

SupramoleculeName: TRPC4 -tetramer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Transient receptor potential cation channel subfamily c member 4a

MacromoleculeName: Transient receptor potential cation channel subfamily c member 4a
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 108.281016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGHHHHHHHH GGSENLYFQG GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPL GRTALLIAIE NENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF T PDITPIIL ...String:
MGHHHHHHHH GGSENLYFQG GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPL GRTALLIAIE NENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF T PDITPIIL AAHTNNYEII KMLVQKGVSV PQPHEVRCNC VECVSSSDVD SLRHSRSRLN IYKALASPSL IALSSEDPFL TA FQLSWEL QELSKVENEF KAEYEELSHQ CKHFAKDLLD QTRSSRELEL ILNFRDDMNL LQDEANNELA RLKLAIKYRQ KEF VAQPNC QQLLASRWYD EFPGWRRRHW AGKLITCVFI GLMFPLLSLC YLVAPKSRYG LFIRKPFIKF ICHTASYLTF LFLL LLASQ HIVSNNPDRQ GPKPTTVEWM ILPWVLGFIW TEIKQMWDGG FQDYIHDWWN LMDFVMNSLY LATISLKIVA YVKYS GCKP RDTWEMWHPT LVAEAVFAIA NIFSSLRLIS LFTANSHLGP LQISLGRMLL DILKFLFIYC LVLLAFANGL NQLYFY YEN SEGMTCKGIR CERQNNAFST LFETLQSLFW SIFGLISLYV TNVKADHKFT EFVGATMFGT YNVISLVVLL NMLIAMM NN SYQHIADHAD IEWKFARTKL WMSYFEEGGT LPPPFNIIPS PKSICYLITW IKVHVFKRRS KRTETFGTLG RRAAENVR L NHQYQEVLRN LVKRYVAAMI RDAKTEEGLT EENFKELKQD ISSFRYEVIG MMKGNRKSTR ANKSDTSASD VSHPEGSLQ YSSALKQNSK LHLYDVTTAL QQQNSEEAKA SLGCLANGSA VVLTEPILKD KARSDFPKDF TDFGLFPKKQ NPNKIYSLAE EATESDPDI LDWGKEDKPL AGKVEQDVNE SKCLMEEDER VLEEQEMEHI ASSHEHLEVL FQ

UniProtKB: Short transient receptor potential channel 4b

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Macromolecule #2: (Z)-7-(4-chlorobenzyl)-1-(3-hydroxypropyl)-3-methyl-8-(4-(phenyld...

MacromoleculeName: (Z)-7-(4-chlorobenzyl)-1-(3-hydroxypropyl)-3-methyl-8-(4-(phenyldiazenyl)-3-(trifluoromethoxy)phenoxy)-3,7-dihydro-1H-purine-2,6-dione
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1IGY
Molecular weightTheoretical: 628.986 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.45 mg/mL
BufferpH: 8.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification done at liquid nitrogen temperature.
DetailsSample was homogenous

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 93.0 K / Max: 113.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3311 / Average exposure time: 3.5 sec. / Average electron dose: 56.0 e/Å2 / Details: Images were collected in movie mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0700000000000003 µm / Calibrated defocus min: 0.49 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 55000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 232983
CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab inito model from Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Software - details: Non uniform refinement / Number images used: 93651
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.0) / Details: SGD algorthim implemented in cryosparc
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 50000 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6g1k


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsPhenix
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 57.21
Output model

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

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