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- EMDB-4339: Electron cryo-microscopy structure of the canonical TRPC4 ion channel -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-4339
TitleElectron cryo-microscopy structure of the canonical TRPC4 ion channel
Map data
Sample
  • Organelle or cellular component: TRPC4
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate
Function / homology
Function and homology information


store-operated calcium channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / monoatomic cation transport / monoatomic cation channel activity / regulation of cytosolic calcium ion concentration / 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
Transient receptor potential cation channel subfamily c member 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsVinayagam D / Mager T / Apelbaum A / Bothe A / Merino F / Hofnagel O / Gatsogiannis C / Raunser S
CitationJournal: Elife / Year: 2018
Title: Electron cryo-microscopy structure of the canonical TRPC4 ion channel.
Authors: Deivanayagabarathy Vinayagam / Thomas Mager / Amir Apelbaum / Arne Bothe / Felipe Merino / Oliver Hofnagel / Christos Gatsogiannis / Stefan Raunser /
Abstract: Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca signaling and have been proposed to act as store-operated channels (SOC). ...Canonical transient receptor channels (TRPC) are non-selective cation channels. They are involved in receptor-operated Ca 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.
History
DepositionMar 21, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseMay 2, 2018-
UpdateAug 1, 2018-
Current statusAug 1, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6g1k
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4339.png

Downloads & links

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Map

FileDownload / File: emd_4339.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 224 pix.
= 244.16 Å		1.09 Å/pix.
x 224 pix.
= 244.16 Å		1.09 Å/pix.
x 224 pix.
= 244.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.042099435 - 0.08184739
Average (Standard dev.)0.00033937985 (±0.003202249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 244.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z244.160244.160244.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0420.0820.000

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Supplemental data

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Sample components

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Entire : TRPC4

EntireName: TRPC4
Components
  • Organelle or cellular component: TRPC4
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

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Supramolecule #1: TRPC4

SupramoleculeName: TRPC4 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Membrane protein
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 432 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 GnTI- / Recombinant plasmid: pEG BacMam

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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: 105.9345 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPLG RTALLIAIEN ENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF TPDITPIILA AHTNNYEIIK M LVQKGVSV ...String:
GSQLYFRRTD NSSYRDRIPL RIVRAESELS TQEKSYLSAV EKGDYASVKL ALEEAEIYFK ININCIDPLG RTALLIAIEN ENLEIIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSDF TPDITPIILA AHTNNYEIIK M LVQKGVSV PQPHEVRCNC VECVSSSDVD SLRHSRSRLN IYKALASPSL IALSSEDPFL TAFQLSWELQ ELSKVENEFK AE YEELSHQ CKHFAKDLLD QTRSSRELEL ILNFRDDMNL LQDEANNELA RLKLAIKYRQ KEFVAQPNCQ QLLASRWYDE FPG WRRRHW AGKLITCVFI GLMFPLLSLC YLVAPKSRYG LFIRKPFIKF ICHTASYLTF LFLLLLASQH IVSNNPDRQG PKPT TVEWM ILPWVLGFIW TEIKQMWDGG FQDYIHDWWN LMDFVMNSLY LATISLKIVA YVKYSGCKPR DTWEMWHPTL VAEAV FAIA NIFSSLRLIS LFTANSHLGP LQISLGRMLL DILKFLFIYC LVLLAFANGL NQLYFYYENS EGMTCKGIRC ERQNNA FST LFETLQSLFW SIFGLISLYV TNVKADHKFT EFVGATMFGT YNVISLVVLL NMLIAMMNNS YQHIADHADI EWKFART KL WMSYFEEGGT LPPPFNIIPS PKSICYLITW IKVHVFKRRS KRTETFGTLG RRAAENVRLN HQYQEVLRNL VKRYVAAM I RDAKTEEGLT EENFKELKQD ISSFRYEVIG MMKGNRKSTR ANKSDTSASD VSHPEGSLQY SSALKQNSKL HLYDVTTAL QQQNSEEAKA SLGCLANGSA VVLTEPILKD KARSDFPKDF TDFGLFPKKQ NPNKIYSLAE EATESDPDIL DWGKEDKPLA GKVEQDVNE SKCLMEEDER VLEEQEMEHI ASSHEHLEVL FQ

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate

MacromoleculeName: (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / type: ligand / ID: 3 / Number of copies: 4 / Formula: 44E
Molecular weightTheoretical: 368.36 Da
Chemical component information

ChemComp-44E:
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / phospholipid*YM

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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

Concentration0.25 mg/mL
BufferpH: 7.4 / Component - Name: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: CS corrected Microscope
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 4 / Number real images: 3890 / Average exposure time: 12.0 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.931 µm / Calibrated defocus min: 0.844 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
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: 426377
CTF correctionSoftware - Name: SPHIRE (ver. 1.0) / Software - details: CTER
Startup modelType of model: NONE / Details: VIPER model
Final reconstructionNumber classes used: 6 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.0) / Number images used: 132622
Initial angle assignmentType: OTHER / Software - Name: SPHIRE (ver. 1.0) / Software - details: RVIPER / Details: VIPER METHOD
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.9375 degrees
Software - Name: SPHIRE (ver. 1.0) / Software - details: MERIDIEN
Final 3D classificationNumber classes: 6 / Avg.num./class: 20000 / Software - Name: SPHIRE (ver. 1.0) / Software - details: SORT3D DEPTH / Details: SORT3D DEPTH

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Atomic model buiding 1

Initial model
PDB IDChain

5vkq

residue_range: 1264-1587

3j5q

residue_range: 429-711
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 90.04 / Target criteria: Real-space correlation
Output model

PDB-6g1k:
Electron cryo-microscopy structure of the canonical TRPC4 ion channel

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