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- EMDB-11968: TRPC4 in LMNG detergent -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-11968
TitleTRPC4 in LMNG detergent
Map data
Sample
  • Organelle or cellular component: TRPC4 membrane protein
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: CALCIUM IONCalcium
KeywordsION CHANNEL / TRPC4 / LMNG / MEMBRANE PROTEIN / TRANSPORT 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
Transient receptor potential cation channel subfamily c member 4a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsVinayagam D / Quentin D
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Elife / Year: 2020
Title: Structural basis of TRPC4 regulation by calmodulin and pharmacological agents.
Authors: Deivanayagabarathy Vinayagam / Dennis Quentin / Jing Yu-Strzelczyk / Oleg Sitsel / Felipe Merino / Markus Stabrin / Oliver Hofnagel / Maolin Yu / Mark W Ledeboer / Georg Nagel / Goran ...Authors: Deivanayagabarathy Vinayagam / Dennis Quentin / Jing Yu-Strzelczyk / Oleg Sitsel / Felipe Merino / Markus Stabrin / Oliver Hofnagel / Maolin Yu / Mark W Ledeboer / Georg Nagel / Goran Malojcic / Stefan Raunser /
Abstract: Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca signaling. Inhibition of TRPCs by small molecules was shown to be promising in ...Canonical transient receptor potential channels (TRPC) are involved in receptor-operated and/or store-operated Ca signaling. Inhibition of TRPCs by small molecules was shown to be promising in treating renal diseases. In cells, the channels are regulated by calmodulin (CaM). Molecular details of both CaM and drug binding have remained elusive so far. Here, we report structures of TRPC4 in complex with three pyridazinone-based inhibitors and CaM. The structures reveal that all the inhibitors bind to the same cavity of the voltage-sensing-like domain and allow us to describe how structural changes from the ligand-binding site can be transmitted to the central ion-conducting pore of TRPC4. CaM binds to the rib helix of TRPC4, which results in the ordering of a previously disordered region, fixing the channel in its closed conformation. This represents a novel CaM-induced regulatory mechanism of canonical TRP channels.
History
DepositionNov 20, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0062
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0062
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b0j
  • Surface level: 0.0062
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11968.png

Downloads & links

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Map

FileDownload / File: emd_11968.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.0062 / Movie #1: 0.0062
Minimum - Maximum-0.025910515 - 0.046326257
Average (Standard dev.)0.000090083806 (±0.0014491762)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0260.0460.000

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Supplemental data

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Sample components

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Entire : TRPC4 membrane protein

EntireName: TRPC4 membrane protein
Components
  • Organelle or cellular component: TRPC4 membrane protein
    • Protein or peptide: Transient receptor potential cation channel subfamily c member 4a
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: TRPC4 membrane protein

SupramoleculeName: TRPC4 membrane protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: solubilised in LMNG
Source (natural)Organism: Danio rerio (zebrafish) / Location in cell: plasma membrane
Molecular weightTheoretical: 108 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: 105.204641 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 ASSHEH

UniProtKB: Transient receptor potential cation channel subfamily c member 4a

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Macromolecule #2: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 2 / Number of copies: 4 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3TRIS
150.0 mMNaClSodium chloridesodium chloride
0.003 percentC47H88O26LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.001 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Specialist opticsSpherical aberration corrector: BCOR Cs corrector first generation
Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 160.0 K / Max: 190.0 K
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 3079 / Average exposure time: 10.0 sec. / Average electron dose: 88.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 393632
Startup modelType of model: EMDB MAP
EMDB ID:

4339

Initial angle assignmentType: NOT APPLICABLE / Details: Used EMD-4339 as a reference
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE / Software - details: MERIDIEN
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Software - details: MERIDIEN / Number images used: 126873

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Atomic model buiding 1

Initial modelPDB ID:

6gik


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 49.08 / Target criteria: Correlation coefficient
Output model

PDB-7b0j:
TRPC4 in LMNG detergent

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