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- EMDB-7082: cryo-EM structure of TRPM4 in apo state with long coiled coil at ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7082
Titlecryo-EM structure of TRPM4 in apo state with long coiled coil at 3.5 angstrom resolution
Map dataStructure of TRPM4 in apo state with long coiled coil at 3.5 angstrom
Sample
  • Complex: homotetramer of mouse TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: SODIUM ION
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of atrial cardiac muscle cell action potential / positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization / sodium channel complex / regulation of T cell cytokine production / membrane depolarization during AV node cell action potential / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / voltage-gated monoatomic ion channel activity / ligand-gated calcium channel activity ...positive regulation of atrial cardiac muscle cell action potential / positive regulation of regulation of vascular associated smooth muscle cell membrane depolarization / sodium channel complex / regulation of T cell cytokine production / membrane depolarization during AV node cell action potential / membrane depolarization during bundle of His cell action potential / membrane depolarization during Purkinje myocyte cell action potential / negative regulation of bone mineralization / voltage-gated monoatomic ion channel activity / ligand-gated calcium channel activity / TRP channels / sodium ion import across plasma membrane / regulation of ventricular cardiac muscle cell action potential / calcium-activated cation channel activity / inorganic cation transmembrane transport / dendritic cell chemotaxis / cellular response to ATP / positive regulation of heart rate / regulation of heart rate by cardiac conduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein sumoylation / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / long-term memory / positive regulation of vasoconstriction / positive regulation of adipose tissue development / regulation of membrane potential / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / positive regulation of canonical Wnt signaling pathway / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / adaptive immune response / calmodulin binding / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
TRPM, SLOG domain / : / SLOG in TRPM / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsGuo J / She J
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
Howard Hughes Medical Institute (HHMI) United States
Cancer Prevention and Research Institute of Texas (CPRIT) United States
Virginia Murchison Linthicum Scholar in Medical Research fund United States
CitationJournal: Nature / Year: 2017
Title: Structures of the calcium-activated, non-selective cation channel TRPM4.
Authors: Jiangtao Guo / Ji She / Weizhong Zeng / Qingfeng Chen / Xiao-Chen Bai / Youxing Jiang /
Abstract: TRPM4 is a calcium-activated, phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P) -modulated, non-selective cation channel that belongs to the family of melastatin-related transient receptor ...TRPM4 is a calcium-activated, phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P) -modulated, non-selective cation channel that belongs to the family of melastatin-related transient receptor potential (TRPM) channels. Here we present the electron cryo-microscopy structures of the mouse TRPM4 channel with and without ATP. TRPM4 consists of multiple transmembrane and cytosolic domains, which assemble into a three-tiered architecture. The N-terminal nucleotide-binding domain and the C-terminal coiled-coil participate in the tetrameric assembly of the channel; ATP binds at the nucleotide-binding domain and inhibits channel activity. TRPM4 has an exceptionally wide filter but is only permeable to monovalent cations; filter residue Gln973 is essential in defining monovalent selectivity. The S1-S4 domain and the post-S6 TRP domain form the central gating apparatus that probably houses the Ca- and PtdIns(4,5)P-binding sites. These structures provide an essential starting point for elucidating the complex gating mechanisms of TRPM4 and reveal the molecular architecture of the TRPM family.
History
DepositionOct 20, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseDec 13, 2017-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bcl
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7082.png

Downloads & links

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Map

FileDownload / File: emd_7082.map.gz / Format: CCP4 / Size: 65.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of TRPM4 in apo state with long coiled coil at 3.5 angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 258 pix.
= 276.06 Å		1.07 Å/pix.
x 258 pix.
= 276.06 Å		1.07 Å/pix.
x 258 pix.
= 276.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.08071831 - 0.1683625
Average (Standard dev.)0.00008581033 (±0.008567744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions258258258
Spacing258258258
CellA=B=C: 276.06003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z258258258
origin x/y/z0.0000.0000.000
length x/y/z276.060276.060276.060
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS258258258
D min/max/mean-0.0810.1680.000

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Supplemental data

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Sample components

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Entire : homotetramer of mouse TRPM4

EntireName: homotetramer of mouse TRPM4
Components
  • Complex: homotetramer of mouse TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: SODIUM ION

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Supramolecule #1: homotetramer of mouse TRPM4

SupramoleculeName: homotetramer of mouse TRPM4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Transient receptor potential cation channel subfamily M member 4

MacromoleculeName: Transient receptor potential cation channel subfamily M member 4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 140.922875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVGPEKEQSW IPKIFRKKVC TTFIVDLSDD AGGTLCQCGQ PRDAHPSVAV EDAFGAAVVT EWNSDEHTTE KPTDAYGDLD FTYSGRKHS NFLRLSDRTD PATVYSLVTR SWGFRAPNLV VSVLGGSGGP VLQTWLQDLL RRGLVRAAQS TGAWIVTGGL H TGIGRHVG ...String:
MVGPEKEQSW IPKIFRKKVC TTFIVDLSDD AGGTLCQCGQ PRDAHPSVAV EDAFGAAVVT EWNSDEHTTE KPTDAYGDLD FTYSGRKHS NFLRLSDRTD PATVYSLVTR SWGFRAPNLV VSVLGGSGGP VLQTWLQDLL RRGLVRAAQS TGAWIVTGGL H TGIGRHVG VAVRDHQTAS TGSSKVVAMG VAPWGVVRNR DMLINPKGSF PARYRWRGDP EDGVEFPLDY NYSAFFLVDD GT YGRLGGE NRFRLRFESY VAQQKTGVGG TGIDIPVLLL LIDGDEKMLK RIEDATQAQL PCLLVAGSGG AADCLVETLE DTL APGSGG LRRGEARDRI RRYFPKGDPE VLQAQVERIM TRKELLTVYS SEDGSEEFET IVLRALVKAC GSSEASAYLD ELRL AVAWN RVDIAQSELF RGDIQWRSFH LEASLMDALL NDRPEFVRLL ISHGLSLGHF LTPVRLAQLY SAVSPNSLIR NLLDQ ASHA SSSKSPPVNG TVELRPPNVG QVLRTLLGET CAPRYPARNT RDSYLGQDHR ENDSLLMDWA NKQPSTDASF EQAPWS DLL IWALLLNRAQ MAIYFWEKGS NSVASALGAC LLLRVMARLE SEAEEAARRK DLAATFESMS VDLFGECYHN SEERAAR LL LRRCPLWGEA TCLQLAMQAD ARAFFAQDGV QSLLTQKWWG EMDSTTPIWA LLLAFFCPPL IYTNLIVFRK SEEEPTQK D LDFDMDSSIN GAGPPGTVEP SAKVALERRQ RRRPGRALCC GKFSKRWSDF WGAPVTAFLG NVVSYLLFLL LFAHVLLVD FQPTKPSVSE LLLYFWAFTL LCEELRQGLG GGWGSLASGG RGPDRAPLRH RLHLYLSDTW NQCDLLALTC FLLGVGCRLT PGLFDLGRT VLCLDFMIFT LRLLHIFTVN KQLGPKIVIV SKMMKDVFFF LFFLCVWLVA YGVATEGILR PQDRSLPSIL R RVFYRPYL QIFGQIPQEE MDVALMIPGN CSMERGSWAH PEGPVAGSCV SQYANWLVVL LLIVFLLVAN ILLLNLLIAM FS YTFSKVH GNSDLYWKAQ RYSLIREFHS RPALAPPLII ISHVRLLIKW LRRCRRCRRA NLPASPVFEH FRVCLSKEAE RKL LTWESV HKENFLLAQA RDKRDSDSER LKRTSQKVDT ALKQLGQIRE YDRRLRGLER EVQHCSRVLT WMAEALSHSA LLPP GAPPP PSPTGSKDRN SKAYVDELTS RGRLEVLFQG PDYKDDDDKH HHHHHHHHH

UniProtKB: Transient receptor potential cation channel subfamily M member 4

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
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: 8 / Component:
ConcentrationFormula
20.0 mMTris
150.0 mMNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsprotein samples are reconstituted into nanodiscs

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3000 / Average exposure time: 15.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 46730
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: 743735
Startup modelType of model: OTHER / Details: The initial model was generated in Relion.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 11545
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2)
Details: Auto-refinement in Relion generated the final reconstruction. The angular sampling was determined automatically in Relion.
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 2)
Details: A focused 3D classification at the coiled coil domain was performed.

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