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

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Basic information

Entry
Database: PDB / ID: 6g1k
TitleElectron cryo-microscopy structure of the canonical TRPC4 ion channel
ComponentsTransient receptor potential cation channel subfamily c member 4a
KeywordsTRANSPORT PROTEIN / ION CHANNEL / TRPC4 / ANKYRIN REPEATS / CIRB DOMAIN / MEMBRANE PROTEIN
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 II / Transient receptor ion channel domain / 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 II / Transient receptor ion channel domain / 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
(2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / CHOLESTEROL HEMISUCCINATE / Transient receptor potential cation channel subfamily c member 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsVinayagam, D. / Mager, T. / Apelbaum, A. / Bothe, A. / Merino, F. / Hofnagel, O. / Gatsogiannis, C. / Raunser, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council615984 Germany
Max Planck Society Germany
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 1, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

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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)427,15812
Polymers423,7384
Non-polymers3,4208
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area40930 Å2
ΔGint-236 kcal/mol
Surface area121870 Å2
MethodPISA

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Components

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


Mass: 105934.500 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 / Details (production host): mammalian expression vector / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney / References: UniProt: U3N7D8
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#3: Chemical
ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H29O8P / Comment: phospholipid*YM

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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 / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Membrane protein / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.432 MDa / Experimental value: NO
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GnTI- / Plasmid: pEG BacMam
Buffer solutionpH: 7.4
Buffer componentName: PBS
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 844 nm / Calibrated defocus max: 2931 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 3890
EM imaging opticsSpherical aberration corrector: CS corrected Microscope

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Processing

EM software
IDNameVersionCategoryDetails
2EPU1.8image acquisition
4SPHIRE1CTF correctionCTER
7UCSF Chimera1.12model fitting
8Rosettamodel fitting
10SPHIRE1initial Euler assignmentRVIPER
11SPHIRE1final Euler assignmentMERIDIEN
12SPHIRE1classificationSORT3D DEPTH
13SPHIRE13D reconstruction
14PHENIX1.13model refinement
15Coot0.8.8model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 426377
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132622 / Algorithm: FOURIER SPACE / Num. of class averages: 6 / Symmetry type: POINT
Atomic model buildingB value: 90.04 / Protocol: OTHER / Space: REAL / Target criteria: Real-space correlation
Atomic model building
IDPDB-ID 3D fitting-IDPdb chain residue range
15VKQ

5vkq

11264-1587
23J5Q

3j5q

1429-711

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