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- EMDB-6911: Cryo-EM structure of human TRPC3 at 4.36A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-6911
TitleCryo-EM structure of human TRPC3 at 4.36A resolution
Map data
Sample
  • Organelle or cellular component: hTRPC3 homo-tetramer
    • Protein or peptide: Short transient receptor potential channel 3
KeywordsTRPC3 channel / MEMBRANE 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 / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / 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 / Elevation of cytosolic Ca2+ levels / Effects of PIP2 hydrolysis / 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 / single fertilization / phototransduction / 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 II / Transient receptor ion channel domain / 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 II / Transient receptor ion channel domain / 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: 4.36 Å
AuthorsChen L / Tang Q
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31521062 China
CitationJournal: Cell Res / Year: 2018
Title: Structure of the receptor-activated human TRPC6 and TRPC3 ion channels.
Authors: Qinglin Tang / Wenjun Guo / Li Zheng / Jing-Xiang Wu / Meng Liu / Xindi Zhou / Xiaolin Zhang / Lei Chen /
Abstract: TRPC6 and TRPC3 are receptor-activated nonselective cation channels that belong to the family of canonical transient receptor potential (TRPC) channels. They are activated by diacylglycerol, a lipid ...TRPC6 and TRPC3 are receptor-activated nonselective cation channels that belong to the family of canonical transient receptor potential (TRPC) channels. They are activated by diacylglycerol, a lipid second messenger. TRPC6 and TRPC3 are involved in many physiological processes and implicated in human genetic diseases. Here we present the structure of human TRPC6 homotetramer in complex with a newly identified high-affinity inhibitor BTDM solved by single-particle cryo-electron microscopy to 3.8 Å resolution. We also present the structure of human TRPC3 at 4.4 Å resolution. These structures show two-layer architectures in which the bell-shaped cytosolic layer holds the transmembrane layer. Extensive inter-subunit interactions of cytosolic domains, including the N-terminal ankyrin repeats and the C-terminal coiled-coil, contribute to the tetramer assembly. The high-affinity inhibitor BTDM wedges between the S5-S6 pore domain and voltage sensor-like domain to inhibit channel opening. Our structures uncover the molecular architecture of TRPC channels and provide a structural basis for understanding the mechanism of these channels.
History
DepositionFeb 11, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseMay 9, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5zbg
  • Surface level: 0.4
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6911.png

Downloads & links

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Map

FileDownload / File: emd_6911.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.5184976 - 1.4565074
Average (Standard dev.)0.020553483 (±0.092056744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 274.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z274.000274.000274.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.5181.4570.021

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Supplemental data

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Sample components

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Entire : hTRPC3 homo-tetramer

EntireName: hTRPC3 homo-tetramer
Components
  • Organelle or cellular component: hTRPC3 homo-tetramer
    • Protein or peptide: Short transient receptor potential channel 3

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Supramolecule #1: hTRPC3 homo-tetramer

SupramoleculeName: hTRPC3 homo-tetramer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 97.465836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGSPSLRRM TVMREKGRRQ AVRGPAFMFN DRGTSLTAEE ERFLDAAEYG NIPVVRKMLE ESKTLNVNCV DYMGQNALQL AVGNEHLEV TELLLKKENL ARIGDALLLA ISKGYVRIVE AILNHPGFAA SKRLTLSPCE QELQDDDFYA YDEDGTRFSP D ITPIILAA ...String:
MEGSPSLRRM TVMREKGRRQ AVRGPAFMFN DRGTSLTAEE ERFLDAAEYG NIPVVRKMLE ESKTLNVNCV DYMGQNALQL AVGNEHLEV TELLLKKENL ARIGDALLLA ISKGYVRIVE AILNHPGFAA SKRLTLSPCE QELQDDDFYA YDEDGTRFSP D ITPIILAA HCQKYEVVHM LLMKGARIER PHDYFCKCGD CMEKQRHDSF SHSRSRINAY KGLASPAYLS LSSEDPVLTA LE LSNELAK LANIEKEFKN DYRKLSMQCK DFVVGVLDLC RDSEEVEAIL NGDLESAEPL EVHRHKASLS RVKLAIKYEV KKF VAHPNC QQQLLTIWYE NLSGLREQTI AIKCLVVLVV ALGLPFLAIG YWIAPCSRLG KILRSPFMKF VAHAASFIIF LGLL VFNAS DRFEGITTLP NITVTDYPKQ IFRVKTTQFT WTEMLIMVWV LGMMWSECKE LWLEGPREYI LQLWNVLDFG MLSIF IAAF TARFLAFLQA TKAQQYVDSY VQESDLSEVT LPPEIQYFTY ARDKWLPSDP QIISEGLYAI AVVLSFSRIA YILPAN ESF GPLQISLGRT VKDIFKFMVL FIMVFFAFMI GMFILYSYYL GAKVNAAFTT VEESFKTLFW SIFGLSEVTS VVLKYDH KF IENIGYVLYG IYNVTMVVVL LNMLIAMINS SYQEIEDDSD VEWKFARSKL WLSYFDDGKT LPPPFSLVPS PKSFVYFI M RIVNFPKCRR RRLQKDIEMG MGNSKSRLNL FTQSNSRVFE SHSFNSILNQ PTRYQQIMKR LIKRYVLKAQ VDKENDEVN EGELKEIKQD ISSLRYELLE DKSQATEELA ILIHKLSEKL NPSMLRCE

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22220

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