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- EMDB-7620: Structure of the human TRPC3 in a lipid-occupied, closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-7620
TitleStructure of the human TRPC3 in a lipid-occupied, closed state
Map dataStructure of the human TRPC3 in a lipid-occupied, closed state
Sample
  • Complex: TRPC3
    • Protein or peptide: Short transient receptor potential channel 3
  • Ligand: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
  • Ligand: (2R)-3-hydroxypropane-1,2-diyl dihexanoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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: 3.3 Å
AuthorsLu W / Du J / Fan C / Choi W
CitationJournal: Elife / Year: 2018
Title: Structure of the human lipid-gated cation channel TRPC3.
Authors: Chen Fan / Wooyoung Choi / Weinan Sun / Juan Du / Wei Lü /
Abstract: The TRPC channels are crucially involved in store-operated calcium entry and calcium homeostasis, and they are implicated in human diseases such as neurodegenerative disease, cardiac hypertrophy, and ...The TRPC channels are crucially involved in store-operated calcium entry and calcium homeostasis, and they are implicated in human diseases such as neurodegenerative disease, cardiac hypertrophy, and spinocerebellar ataxia. We present a structure of the full-length human TRPC3, a lipid-gated TRPC member, in a lipid-occupied, closed state at 3.3 Angstrom. TRPC3 has four elbow-like membrane reentrant helices prior to the first transmembrane helix. The TRP helix is perpendicular to, and thus disengaged from, the pore-lining S6, suggesting a different gating mechanism from other TRP subfamily channels. The third transmembrane helix S3 is remarkably long, shaping a unique transmembrane domain, and constituting an extracellular domain that may serve as a sensor of external stimuli. We identified two lipid-binding sites, one being sandwiched between the pre-S1 elbow and the S4-S5 linker, and the other being close to the ion-conducting pore, where the conserved LWF motif of the TRPC family is located.
History
DepositionMar 25, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseMay 16, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cud
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7620.png

Downloads & links

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Map

FileDownload / File: emd_7620.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the human TRPC3 in a lipid-occupied, closed state
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.07392642 - 0.18155782
Average (Standard dev.)-0.002542153 (±0.0041286475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 412.41602 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z412.416412.416412.416
α/β/γ90.00090.00090.000
start NX/NY/NZ-2216-4
NX/NY/NZ376362
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0740.182-0.003

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Supplemental data

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Sample components

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Entire : TRPC3

EntireName: TRPC3
Components
  • Complex: TRPC3
    • Protein or peptide: Short transient receptor potential channel 3
  • Ligand: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
  • Ligand: (2R)-3-hydroxypropane-1,2-diyl dihexanoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TRPC3

SupramoleculeName: TRPC3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 390 KDa

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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: 92.691242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MREKGRRQAV RGPAFMFNDR GTSLTAEEER FLDAAEYGNI PVVRKMLEES KTLNVNCVDY MGQNALQLAV GNEHLEVTEL LLKKENLAR IGDALLLAIS KGYVRIVEAI LNHPGFAASK RLTLSPCEQE LQDDDFYAYD EDGTRFSPDI TPIILAAHCQ K YEVVHMLL ...String:
MREKGRRQAV RGPAFMFNDR GTSLTAEEER FLDAAEYGNI PVVRKMLEES KTLNVNCVDY MGQNALQLAV GNEHLEVTEL LLKKENLAR IGDALLLAIS KGYVRIVEAI LNHPGFAASK RLTLSPCEQE LQDDDFYAYD EDGTRFSPDI TPIILAAHCQ K YEVVHMLL MKGARIERPH DYFCKCGDCM EKQRHDSFSH SRSRINAYKG LASPAYLSLS SEDPVLTALE LSNELAKLAN IE KEFKNDY RKLSMQCKDF VVGVLDLCRD SEEVEAILNG DLESAEPLEV HRHKASLSRV KLAIKYEVKK FVAHPNCQQQ LLT IWYENL SGLREQTIAI KCLVVLVVAL GLPFLAIGYW IAPCSRLGKI LRSPFMKFVA HAASFIIFLG LLVFNASDRF EGIT TLPNI TVTDYPKQIF RVKTTQFTWT EMLIMVWVLG MMWSECKELW LEGPREYILQ LWNVLDFGML SIFIAAFTAR FLAFL QATK AQQYVDSYVQ ESDLSEVTLP PEIQYFTYAR DKWLPSDPQI ISEGLYAIAV VLSFSRIAYI LPANESFGPL QISLGR TVK DIFKFMVLFI MVFFAFMIGM FILYSYYLGA KVNAAFTTVE ESFKTLFWSI FGLSEVTSVV LKYDHKFIEN IGYVLYG IY NVTMVVVLLN MLIAMINSSY QEIEDDSDVE WKFARSKLWL SYFDDGKTLP PPFSLVPSPK SFVYFIMRIV NFPKCRRR R LQKDIEMGMG NSKSRLNLFT QSNSRVFESH SFNSILNQPT RYQQIMKRLI KRYVLKAQVD KENDEVNEGE LKEIKQDIS SLRYEL

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Macromolecule #2: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoylo...

MacromoleculeName: (2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate
type: ligand / ID: 2 / Number of copies: 4 / Formula: 6OE
Molecular weightTheoretical: 411.428 Da
Chemical component information

ChemComp-6OE:
(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate

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Macromolecule #3: (2R)-3-hydroxypropane-1,2-diyl dihexanoate

MacromoleculeName: (2R)-3-hydroxypropane-1,2-diyl dihexanoate / type: ligand / ID: 3 / Number of copies: 4 / Formula: FGJ
Molecular weightTheoretical: 288.38 Da
Chemical component information

ChemComp-FGJ:
(2R)-3-hydroxypropane-1,2-diyl dihexanoate

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: 8
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: 6.76 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9) / Number images used: 143855

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