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- EMDB-7823: Cytoplasmic domain of TRPC3 -

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Basic information

Entry
Database: EMDB / ID: EMD-7823
TitleCytoplasmic domain of TRPC3
Map dataCytoplasmic domain of TRPC3
Sample
  • Complex: Cytoplasmic domain of TRPC3 homotetramer
    • Protein or peptide: Short transient receptor potential channel 3
KeywordsTRP channel / Ion Channel / Membrane protein / cerebellum / moonwalker / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / TRP channels / positive regulation of calcium ion transport into cytosol ...positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / TRP channels / positive regulation of calcium ion transport into cytosol / response to ATP / phototransduction / single fertilization / MECP2 regulates neuronal receptors and channels / regulation of cytosolic calcium ion concentration / calcium ion transmembrane transport / calcium channel activity / response to calcium ion / calcium ion transport / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSierra-Valdez FJ / Azumaya CM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01HD061543 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125629 United States
CitationJournal: J Biol Chem / Year: 2018
Title: Structure-function analyses of the ion channel TRPC3 reveal that its cytoplasmic domain allosterically modulates channel gating.
Authors: Francisco Sierra-Valdez / Caleigh M Azumaya / Luis O Romero / Terunaga Nakagawa / Julio F Cordero-Morales /
Abstract: The transient receptor potential ion channels support Ca permeation in many organs, including the heart, brain, and kidney. Genetic mutations in transient receptor potential cation channel subfamily ...The transient receptor potential ion channels support Ca permeation in many organs, including the heart, brain, and kidney. Genetic mutations in transient receptor potential cation channel subfamily C member 3 (TRPC3) are associated with neurodegenerative diseases, memory loss, and hypertension. To better understand the conformational changes that regulate TRPC3 function, we solved the cryo-EM structures for the full-length human TRPC3 and its cytoplasmic domain (CPD) in the apo state at 5.8- and 4.0-Å resolution, respectively. These structures revealed that the TRPC3 transmembrane domain resembles those of other TRP channels and that the CPD is a stable module involved in channel assembly and gating. We observed the presence of a C-terminal domain swap at the center of the CPD where horizontal helices (HHs) transition into a coiled-coil bundle. Comparison of TRPC3 structures revealed that the HHs can reside in two distinct positions. Electrophysiological analyses disclosed that shortening the length of the C-terminal loop connecting the HH with the TRP helices increases TRPC3 activity and that elongating the length of the loop has the opposite effect. Our findings indicate that the C-terminal loop affects channel gating by altering the allosteric coupling between the cytoplasmic and transmembrane domains. We propose that molecules that target the HH may represent a promising strategy for controlling TRPC3-associated neurological disorders and hypertension.
History
DepositionApr 25, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseAug 29, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0448
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0448
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6d7l
  • Surface level: 0.0448
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7823.png

Downloads & links

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Map

FileDownload / File: emd_7823.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytoplasmic domain of TRPC3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 280.576 Å		1.1 Å/pix.
x 256 pix.
= 280.576 Å		1.1 Å/pix.
x 256 pix.
= 280.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0448 / Movie #1: 0.0448
Minimum - Maximum-0.092570335 - 0.1549892
Average (Standard dev.)0.00045253965 (±0.004949564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.576 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z280.576280.576280.576
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0930.1550.000

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Supplemental data

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Mask #1

Fileemd_7823_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap for cytoplasmic domain of TRPC3

Fileemd_7823_half_map_1.map
AnnotationHalfmap for cytoplasmic domain of TRPC3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap2 for cytoplasmic domain of TRPC3

Fileemd_7823_half_map_2.map
AnnotationHalfmap2 for cytoplasmic domain of TRPC3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cytoplasmic domain of TRPC3 homotetramer

EntireName: Cytoplasmic domain of TRPC3 homotetramer
Components
  • Complex: Cytoplasmic domain of TRPC3 homotetramer
    • Protein or peptide: Short transient receptor potential channel 3

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Supramolecule #1: Cytoplasmic domain of TRPC3 homotetramer

SupramoleculeName: Cytoplasmic domain of TRPC3 homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 097 kDa/nm

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Macromolecule #1: Short transient receptor potential channel 3

MacromoleculeName: Short transient receptor potential channel 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.869281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAMGSMEGSP SLRRMTVMRE KGRRQAVRGP AFMFNDRGTS LTAEEERFLD AAEYGNIPVV RKMLEESKTL NVNCVDYMGQ NALQLAVGN EHLEVTELLL KKENLARIGD ALLLAISKGY VRIVEAILNH PGFAASKRLT LSPCEQELQD DDFYAYDEDG T RFSPDITP ...String:
GAMGSMEGSP SLRRMTVMRE KGRRQAVRGP AFMFNDRGTS LTAEEERFLD AAEYGNIPVV RKMLEESKTL NVNCVDYMGQ NALQLAVGN EHLEVTELLL KKENLARIGD ALLLAISKGY VRIVEAILNH PGFAASKRLT LSPCEQELQD DDFYAYDEDG T RFSPDITP IILAAHCQKY EVVHMLLMKG ARIERPHDYF CKCGDCMEKQ RHDSFSHSRS RINAYKGLAS PAYLSLSSED PV LTALELS NELAKLANIE KEFKNDYRKL SMQCKDFVVG VLDLCRDSEE VEAILNGDLE SAEPLEVHRH KASLSRVKLA IKY EVKKFV AHPNCQQQLL TIWYENLSGL REQTIAIKCL VVLVVALGLP FLAIGYWIAP CSRLGKILRS PFMKFVAHAA SFII FLGLL VFNASDRFEG ITTLPNITVT DYPKQIFRVK TTQFTWTEML IMVWVLGMMW SECKELWLEG PREYILQLWN VLDFG MLSI FIAAFTARFL AFLQATKAQQ YVDSYVQESD LSEVTLPPEI QYFTYARDKW LPSDPQIISE GLYAIAVVLS FSRIAY ILP ANESFGPLQI SLGRTVKDIF KFMVLFIMVF FAFMIGMFIL YSYYLGAKVN AAFTTVEESF KTLFWSIFGL SEVTSVV LK YDHKFIENIG YVLYGIYNVT MVVVLLNMLI AMINSSYQEI EDDSDVEWKF ARSKLWLSYF DDGKTLPPPF SLVPSPKS F VYFIMRIVNF PKCRRRRLQK DIEMGMGNSK SRLNLFTQSN SRVFESHSFN SILNQPTRYQ QIMKRLIKRY VLKAQVDKE NDEVNEGELK EIKQDISSLR YELLEDKSQA TEELAILIHK LSEKLNPSML RCE

UniProtKB: Short transient receptor potential channel 3

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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

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE
DetailsMonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope with Cs corrector was used
Energy filter - Name: GIF Bioquantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1688 / Average exposure time: 7.5 sec. / Average electron dose: 1.63 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 105000
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: 589731
Startup modelType of model: EMDB MAP
EMDB ID:

7637


Details: Our lab's previous submission of the cytoplasmic domain of TRPC6
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 19398
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6d7l:
Cytoplasmic domain of TRPC3

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