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- EMDB-6856: Cryo-EM structure of human TRPC6 at 3.8A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-6856
TitleCryo-EM structure of human TRPC6 at 3.8A resolution
Map data
Sample
  • Organelle or cellular component: hTRPC6 homo-tetramer in complex with inhibitor
    • Protein or peptide: Short transient receptor potential channel 6
KeywordsTRPC6 channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of ion transmembrane transporter activity / slit diaphragm / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / cation channel complex ...positive regulation of ion transmembrane transporter activity / slit diaphragm / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / positive regulation of calcium ion transport / cation channel complex / actinin binding / clathrin binding / TRP channels / monoatomic cation transport / regulation of cytosolic calcium ion concentration / single fertilization / monoatomic cation channel activity / positive regulation of neuron differentiation / calcium ion transmembrane transport / calcium channel activity / cellular response to hydrogen peroxide / neuron differentiation / actin binding / positive regulation of cytosolic calcium ion concentration / ATPase binding / cellular response to hypoxia / protein homodimerization activity / membrane / plasma membrane / cytoplasm
Similarity search - Function
Transient receptor potential channel, canonical 6 / 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 profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...Transient receptor potential channel, canonical 6 / 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 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen L / Tang Q
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
DepositionDec 2, 2017-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 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-5yx9
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_6856.png

Downloads & links

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Map

FileDownload / File: emd_6856.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 200 pix.
= 266. Å		1.33 Å/pix.
x 200 pix.
= 266. Å		1.33 Å/pix.
x 200 pix.
= 266. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.7911449 - 1.6972038
Average (Standard dev.)0.017723903 (±0.0970306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 266.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z266.000266.000266.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.7911.6970.018

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Supplemental data

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Sample components

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Entire : hTRPC6 homo-tetramer in complex with inhibitor

EntireName: hTRPC6 homo-tetramer in complex with inhibitor
Components
  • Organelle or cellular component: hTRPC6 homo-tetramer in complex with inhibitor
    • Protein or peptide: Short transient receptor potential channel 6

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Supramolecule #1: hTRPC6 homo-tetramer in complex with inhibitor

SupramoleculeName: hTRPC6 homo-tetramer in complex with inhibitor / 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 6

MacromoleculeName: Short transient receptor potential channel 6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.453242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQSPAFGPR RGSSPRGAAG AAARRNESQD YLLMDSELGE DGCPQAPLPC YGYYPCFRGS DNRLAHRRQT VLREKGRRLA NRGPAYMFS DRSTSLSIEE ERFLDAAEYG NIPVVRKMLE ECHSLNVNCV DYMGQNALQL AVANEHLEIT ELLLKKENLS R VGDALLLA ...String:
MSQSPAFGPR RGSSPRGAAG AAARRNESQD YLLMDSELGE DGCPQAPLPC YGYYPCFRGS DNRLAHRRQT VLREKGRRLA NRGPAYMFS DRSTSLSIEE ERFLDAAEYG NIPVVRKMLE ECHSLNVNCV DYMGQNALQL AVANEHLEIT ELLLKKENLS R VGDALLLA ISKGYVRIVE AILSHPAFAE GKRLATSPSQ SELQQDDFYA YDEDGTRFSH DVTPIILAAH CQEYEIVHTL LR KGARIER PHDYFCKCND CNQKQKHDSF SHSRSRINAY KGLASPAYLS LSSEDPVMTA LELSNELAVL ANIEKEFKND YKK LSMQCK DFVVGLLDLC RNTEEVEAIL NGDVETLQSG DHGRPNLSRL KLAIKYEVKK FVAHPNCQQQ LLSIWYENLS GLRQ QTMAV KFLVVLAVAI GLPFLALIYW FAPCSKMGKI MRGPFMKFVA HAASFTIFLG LLVMNAADRF EGTKLLPNET STDNA KQLF RMKTSCFSWM EMLIISWVIG MIWAECKEIW TQGPKEYLFE LWNMLDFGML AIFAASFIAR FMAFWHASKA QSIIDA NDT LKDLTKVTLG DNVKYYNLAR IKWDPSDPQI ISEGLYAIAV VLSFSRIAYI LPANESFGPL QISLGRTVKD IFKFMVI FI MVFVAFMIGM FNLYSYYIGA KQNEAFTTVE ESFKTLFWAI FGLSEVKSVV INYNHKFIEN IGYVLYGVYN VTMVIVLL N MLIAMINSSF QEIEDDADVE WKFARAKLWF SYFEEGRTLP VPFNLVPSPK SLFYLLLKLK KWISELFQGH KKGFQEDAE MNKINEEKKL GILGSHEDLS KLSLDKKQVG HNKQPSIRSS EDFHLNSFNN PPRQYQKIMK RLIKRYVLQA QIDKESDEVN EGELKEIKQ DISSLRYELL EEKSQNTEDL AELIRELGEK LSMEPNQEET NR

UniProtKB: Short transient receptor potential channel 6

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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53528
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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