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- EMDB-6901: Structure of the mouse TRPC4 ion channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6901
TitleStructure of the mouse TRPC4 ion channel
Map data
Sample
  • Complex: Mouse TRPC4
    • Protein or peptide: Short transient receptor potential channel 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: SODIUM ION
KeywordsCryoEM / mouse full length TRPC4 / MEMBRANE PROTEIN
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / store-operated calcium channel activity / TRP channels / inositol 1,4,5 trisphosphate binding / calcium ion import / cortical cytoskeleton / oligodendrocyte differentiation / calcium channel complex / caveola / beta-catenin binding ...gamma-aminobutyric acid secretion / store-operated calcium channel activity / TRP channels / inositol 1,4,5 trisphosphate binding / calcium ion import / cortical cytoskeleton / oligodendrocyte differentiation / calcium channel complex / caveola / beta-catenin binding / cell-cell junction / basolateral plasma membrane / cadherin binding / membrane raft / cell surface / protein-containing complex / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 4 / 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 repeat region circular profile. / ankyrin repeats ...Transient receptor potential channel, canonical 4 / 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 repeat region circular 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 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsDuan J / Li Z
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the mouse TRPC4 ion channel.
Authors: Jingjing Duan / Jian Li / Bo Zeng / Gui-Lan Chen / Xiaogang Peng / Yixing Zhang / Jianbin Wang / David E Clapham / Zongli Li / Jin Zhang /
Abstract: Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally mediated hot and cold sensation to intracellular organellar ...Members of the transient receptor potential (TRP) ion channels conduct cations into cells. They mediate functions ranging from neuronally mediated hot and cold sensation to intracellular organellar and primary ciliary signaling. Here we report a cryo-electron microscopy (cryo-EM) structure of TRPC4 in its unliganded (apo) state to an overall resolution of 3.3 Å. The structure reveals a unique architecture with a long pore loop stabilized by a disulfide bond. Beyond the shared tetrameric six-transmembrane fold, the TRPC4 structure deviates from other TRP channels with a unique cytosolic domain. This unique cytosolic N-terminal domain forms extensive aromatic contacts with the TRP and the C-terminal domains. The comparison of our structure with other known TRP structures provides molecular insights into TRPC4 ion selectivity and extends our knowledge of the diversity and evolution of the TRP channels.
History
DepositionFeb 2, 2018-
Header (metadata) releaseApr 18, 2018-
Map releaseApr 18, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5z96
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6901.png

Downloads & links

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Map

FileDownload / File: emd_6901.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.16160044 - 0.23601964
Average (Standard dev.)0.00022500352 (±0.0060111345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1620.2360.000

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Supplemental data

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Sample components

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Entire : Mouse TRPC4

EntireName: Mouse TRPC4
Components
  • Complex: Mouse TRPC4
    • Protein or peptide: Short transient receptor potential channel 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
  • Ligand: SODIUM ION

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Supramolecule #1: Mouse TRPC4

SupramoleculeName: Mouse TRPC4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Short transient receptor potential channel 4

MacromoleculeName: Short transient receptor potential channel 4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 87.561516 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQFYYKRNV NAPYRDRIPL RIVRAESELS PSEKAYLNAV EKGDYASVKK SLEEAEIYFK ININCIDPLG RTALLIAIEN ENLELIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSEF TPDITPIILA AHTNNYEIIK L LVQKGVSV ...String:
MAQFYYKRNV NAPYRDRIPL RIVRAESELS PSEKAYLNAV EKGDYASVKK SLEEAEIYFK ININCIDPLG RTALLIAIEN ENLELIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSEF TPDITPIILA AHTNNYEIIK L LVQKGVSV PRPHEVRCNC VECVSSSDVD SLRHSRSRLN IYKALASPSL IALSSEDPFL TAFQLSWELQ ELSKVENEFK SE YEELSRQ CKQFAKDLLD QTRSSRELEI ILNYRDDNSL IEEQSGNDLA RLKLAIKYRQ KEFVAQPNCQ QLLASRWYDE FPG WRRRHW AVKMVTCFII GLLFPVFSVC YLIAPKSPLG LFIRKPFIKF ICHTASYLTF LFLLLLASQH IDRSDLNRQG PPPT IVEWM ILPWVLGFIW GEIKQMWDGG LQDYIHDWWN LMDFVMNSLY LATISLKIVA FVKYSALNPR ESWDMWHPTL VAEAL FAIA NIFSSLRLIS LFTANSHLGP LQISLGRMLL DILKFLFIYC LVLLAFANGL NQLYFYYEET KGLSCKGIRC EKQNNA FST LFETLQSLFW SIFGLINLYV TNVKAQHEFT EFVGATMFGT YNVISLVVLL NMLIAMMNNS YQLIADHADI EWKFART KL WMSYFEEGGT LPTPFNVIPS PKSLWYLVKW IWTHLCKKKM RRKPESFGTI GRRAADNLRR HHQYQEVMRN LVKRYVAA M IREAKTEEGL TEENVKELKQ DISSFRFEVL GLLR

UniProtKB: Short transient receptor potential channel 4

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

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 3 / 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 #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 5
Molecular weightTheoretical: 22.99 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 232858
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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