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- EMDB-8871: Cryo-EM structure of a human TRPM4 channel in complex with calciu... -

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Basic information

Entry
Database: EMDB / ID: EMD-8871
TitleCryo-EM structure of a human TRPM4 channel in complex with calcium and decavanadate
Map datamembrane protein
Sample
  • Complex: TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: DECAVANADATE
KeywordsIon channel / MEMBRANE 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 / ligand-gated calcium channel activity / sodium ion import across plasma membrane ...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 / ligand-gated calcium channel activity / 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 / TRP channels / sodium channel activity / 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 / positive regulation of vasoconstriction / positive regulation of adipose tissue development / calcium-mediated signaling / calcium ion transmembrane transport / Sensory perception of sweet, bitter, and umami (glutamate) taste / positive regulation of canonical Wnt signaling pathway / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / adaptive immune response / calmodulin binding / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / Golgi apparatus / endoplasmic reticulum / nucleoplasm / ATP binding / identical protein 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLu W / Winkler PA
CitationJournal: Nature / Year: 2017
Title: Electron cryo-microscopy structure of a human TRPM4 channel.
Authors: Paige A Winkler / Yihe Huang / Weinan Sun / Juan Du / Wei Lü /
Abstract: Ca-activated, non-selective (CAN) ion channels sense increases of the intracellular Ca concentration, producing a flux of Na and/or K ions that depolarizes the cell, thus modulating cellular Ca entry. ...Ca-activated, non-selective (CAN) ion channels sense increases of the intracellular Ca concentration, producing a flux of Na and/or K ions that depolarizes the cell, thus modulating cellular Ca entry. CAN channels are involved in cellular responses such as neuronal bursting activity and cardiac rhythm. Here we report the electron cryo-microscopy structure of the most widespread CAN channel, human TRPM4, bound to the agonist Ca and the modulator decavanadate. Four cytosolic C-terminal domains form an umbrella-like structure with a coiled-coil domain for the 'pole' and four helical 'ribs' spanning the N-terminal TRPM homology regions (MHRs), thus holding four subunits in a crown-like architecture. We observed two decavanadate-binding sites, one in the C-terminal domain and another in the intersubunit MHR interface. A glutamine in the selectivity filter may be an important determinant of monovalent selectivity. Our structure provides new insights into the function and pharmacology of both the CAN and the TRPM families.
History
DepositionAug 3, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseDec 13, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing 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-5wp6
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8871.png

Downloads & links

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Map

FileDownload / File: emd_8871.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmembrane protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 448 pix.
= 487.424 Å		1.09 Å/pix.
x 448 pix.
= 487.424 Å		1.09 Å/pix.
x 448 pix.
= 487.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.051982645 - 0.14532813
Average (Standard dev.)-0.00016861694 (±0.0035422537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 487.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0881.0881.088
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z487.424487.424487.424
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0520.145-0.000

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Supplemental data

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Additional map: membrane protein

Fileemd_8871_additional.map
Annotationmembrane protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPM4

EntireName: TRPM4
Components
  • Complex: TRPM4
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: DECAVANADATE

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Supramolecule #1: TRPM4

SupramoleculeName: TRPM4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 540 KDa

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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: Homo sapiens (human)
Molecular weightTheoretical: 134.456484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVPEKEQSW IPKIFKKKTC TTFIVDSTDP GGTLCQCGRP RTAHPAVAME DAFGAAVVTV WDSDAHTTEK PTDAYGELDF TGAGRKHSN FLRLSDRTDP AAVYSLVTRT WGFRAPNLVV SVLGGSGGPV LQTWLQDLLR RGLVRAAQST GAWIVTGGLH T GIGRHVGV ...String:
MVVPEKEQSW IPKIFKKKTC TTFIVDSTDP GGTLCQCGRP RTAHPAVAME DAFGAAVVTV WDSDAHTTEK PTDAYGELDF TGAGRKHSN FLRLSDRTDP AAVYSLVTRT WGFRAPNLVV SVLGGSGGPV LQTWLQDLLR RGLVRAAQST GAWIVTGGLH T GIGRHVGV AVRDHQMAST GGTKVVAMGV APWGVVRNRD TLINPKGSFP ARYRWRGDPE DGVQFPLDYN YSAFFLVDDG TH GCLGGEN RFRLRLESYI SQQKTGVGGT GIDIPVLLLL IDGDEKMLTR IENATQAQLP CLLVAGSGGA ADCLAETLED TLA PGSGGA RQGEARDRIR RFFPKGDLEV LQAQVERIMT RKELLTVYSS EDGSEEFETI VLKALVKACG SSEASAYLDE LRLA VAWNR VDIAQSELFR GDIQWRSFHL EASLMDALLN DRPEFVRLLI SHGLSLGHFL TPMRLAQLYS AAPSNSLIRN LLDQA SHSA GTKAPALKGG AAELRPPDVG HVLRMLLGKM CAPRYPSGGA WDPHPGQGFG ESMYLLSDKA TSPLSLDAGL GQAPWS DLL LWALLLNRAQ MAMYFWEMGS NAVSSALGAC LLLRVMARLE PDAEEAARRK DLAFKFEGMG VDLFGECYRS SEVRAAR LL LRRCPLWGDA TCLQLAMQAD ARAFFAQDGV QSLLTQKWWG DMASTTPIWA LVLAFFCPPL IYTRLITFRK SEEEPTRE E LEFDMDSVIN GEGPVGTADP AEKTPLGVPR QSGRPGCCGG RCGGRRCLRR WFHFWGAPVT IFMGNVVSYL LFLLLFSRV LLVDFQPAPP GSLELLLYFW AFTLLCEELR QGLSGGGGSL ASGGPGPGHA SLSQRLRLYL ADSWNQCDLV ALTCFLLGVG CRLTPGLYH LGRTVLCIDF MVFTVRLLHI FTVNKQLGPK IVIVSKMMKD VFFFLFFLGV WLVAYGVATE GLLRPRDSDF P SILRRVFY RPYLQIFGQI PQEDMDVALM EHSNCSSEPG FWAHPPGAQA GTCVSQYANW LVVLLLVIFL LVANILLVNL LI AMFSYTF GKVQGNSDLY WKAQRYRLIR EFHSRPALAP PFIVISHLRL LLRQLCRRPR SPQPSSPALE HFRVYLSKEA ERK LLTWES VHKENFLLAR ARDKRESDSE RLKRTSQKVD LALKQLGHIR EYEQRLKVLE REVQQCSRVL GWVAEALSRS ALLP PGGPP PPDLPGSKD

UniProtKB: Transient receptor potential cation channel subfamily M member 4

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Macromolecule #2: DECAVANADATE

MacromoleculeName: DECAVANADATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: DVT
Molecular weightTheoretical: 957.398 Da
Chemical component information

ChemComp-DVT:
DECAVANADATE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 121906
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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