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- EMDB-7132: Human TRPM4 ion channel in lipid nanodiscs in a calcium-free state -

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Basic information

Entry
Database: EMDB / ID: EMD-7132
TitleHuman TRPM4 ion channel in lipid nanodiscs in a calcium-free state
Map dataSharpened 3D density map of human TRPM4 in lipid nanodisc. This reconstruction includes the whole molecule.
Sample
  • Complex: Human TRPM4 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
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 / TRP channels / dendritic cell chemotaxis / 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 / positive regulation of cell population proliferation / calcium ion binding / 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: 3.2 Å
AuthorsAutzen HE / Myasnikov AG / Campbell MG / Asarnow D / Julius D / Cheng Y
Funding support United States, Denmark, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098672 United States
National Institutes of Health/Office of the DirectorS10OD021741 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
Danish Council of Independent ResearchDFF-5051-00085 Denmark
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS047723 United States
CitationJournal: Science / Year: 2018
Title: Structure of the human TRPM4 ion channel in a lipid nanodisc.
Authors: Henriette E Autzen / Alexander G Myasnikov / Melody G Campbell / Daniel Asarnow / David Julius / Yifan Cheng /
Abstract: Transient receptor potential (TRP) melastatin 4 (TRPM4) is a widely expressed cation channel associated with a variety of cardiovascular disorders. TRPM4 is activated by increased intracellular ...Transient receptor potential (TRP) melastatin 4 (TRPM4) is a widely expressed cation channel associated with a variety of cardiovascular disorders. TRPM4 is activated by increased intracellular calcium in a voltage-dependent manner but, unlike many other TRP channels, is permeable to monovalent cations only. Here we present two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo-electron microscopy. These structures, with and without calcium bound, reveal a general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain. The structures correspond to two distinct closed states. Calcium binding induces conformational changes that likely prime the channel for voltage-dependent opening.
History
DepositionNov 28, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseDec 20, 2017-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bqr
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7132.png

Downloads & links

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Map

FileDownload / File: emd_7132.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened 3D density map of human TRPM4 in lipid nanodisc. This reconstruction includes the whole molecule.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å		1.05 Å/pix.
x 320 pix.
= 334.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4 / Movie #1: 4
Minimum - Maximum-26.505821 - 41.100292
Average (Standard dev.)-0.00000001091 (±1.0000194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0461.0461.046
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z334.720334.720334.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-26.50641.100-0.000

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Supplemental data

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Additional map: Unsharpened 3D density map of human TRPM4 in...

Fileemd_7132_additional_1.map
AnnotationUnsharpened 3D density map of human TRPM4 in lipid nanodisc. The reconstruction includes the whole molecule.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened 3D density map of human TRPM4 in...

Fileemd_7132_additional_2.map
AnnotationSharpened 3D density map of human TRPM4 in lipid nanodisc. This reconstruction includes only the cytoplasmic domain refined as a monomer, showing connectivity but fewer high-resolution features.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened 3D density map of human TRPM4 in...

Fileemd_7132_additional_3.map
AnnotationSharpened 3D density map of human TRPM4 in lipid nanodisc. The reconstruction includes only the transmembrane domain and part of the cytoplasmic domain, refined with C4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened 3D density map of human TRPM4 in...

Fileemd_7132_additional_4.map
AnnotationSharpened 3D density map of human TRPM4 in lipid nanodisc. This reconstruction includes only the cytoplasmic domain refined as a monomer, showing high-resolution features but less connectivity.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened 3D density half map #1 of human...

Fileemd_7132_half_map_1.map
AnnotationUnsharpened 3D density half map #1 of human TRPM4 in lipid nanodisc. The reconstruction includes the whole molecule.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened 3D density half map #2 of human...

Fileemd_7132_half_map_2.map
AnnotationUnsharpened 3D density half map #2 of human TRPM4 in lipid nanodisc. The reconstruction includes the whole molecule.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human TRPM4 ion channel

EntireName: Human TRPM4 ion channel
Components
  • Complex: Human TRPM4 ion channel
    • Protein or peptide: Transient receptor potential cation channel subfamily M member 4
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Human TRPM4 ion channel

SupramoleculeName: Human TRPM4 ion channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Human TRPM4 ion channel in lipid nanodiscs in a calcium-free state
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightExperimental: 134.6 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: 121.477953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YGELDFTGAG RKHSNFLRLS DRTDPAAVYS LVTRTWGFRA PNLVVSVLGG SGGPVLQTWL QDLLRRGLVR AAQSTGAWIV TGGLHTGIG RHVGVAVRDH QMASTGGTKV VAMGVAPWGV VRNRDTLINP KGSFPARYRW RGDPEDGVQF PLDYNYSAFF L VDDGTHGC ...String:
YGELDFTGAG RKHSNFLRLS DRTDPAAVYS LVTRTWGFRA PNLVVSVLGG SGGPVLQTWL QDLLRRGLVR AAQSTGAWIV TGGLHTGIG RHVGVAVRDH QMASTGGTKV VAMGVAPWGV VRNRDTLINP KGSFPARYRW RGDPEDGVQF PLDYNYSAFF L VDDGTHGC LGGENRFRLR LESYISQQKT GVGGTGIDIP VLLLLIDGDE KMLTRIENAT QAQLPCLLVA GSGGAADCLA ET LEDTLAP GSGGARQGEA RDRIRRFFPK GDLEVLQAQV ERIMTRKELL TVYSSEDGSE EFETIVLKAL VKACGSSEAS AYL DELRLA VAWNRVDIAQ SELFRGDIQW RSFHLEASLM DALLNDRPEF VRLLISHGLS LGHFLTPMRL AQLYSAAPSN SLIR NLLDQ ASHSAGTKAP ALKGGAAELR PPDVGHVLRM LLGKMCAPRY PSGGAWDPHP GQGFGESMYL LSDKATSPLS LDAGL GQAP WSDLLLWALL LNRAQMAMYF WEMGSNAVSS ALGACLLLRV MARLEPDAEE AARRKDLAFK FEGMGVDLFG ECYRSS EVR AARLLLRRCP LWGDATCLQL AMQADARAFF AQDGVQSLLT QKWWGDMAST TPIWALVLAF FCPPLIYTRL ITFRKSE EE PTREELEFDM DSVINGEGPV GTADPAEKTP LGVPRQSGRP GCCGGRCGGR RCLRRWFHFW GAPVTIFMGN VVSYLLFL L LFSRVLLVDF QPAPPGSLEL LLYFWAFTLL CEELRQGLSG GGGSLASGGP GPGHASLSQR LRLYLADSWN QCDLVALTC FLLGVGCRLT PGLYHLGRTV LCIDFMVFTV RLLHIFTVNK QLGPKIVIVS KMMKDVFFFL FFLGVWLVAY GVATEGLLRP RDSDFPSIL RRVFYRPYLQ IFGQIPQEDM DVALMEHSNC SSEPGFWAHP PGAQAGTCVS QYANWLVVLL LVIFLLVANI L LVNLLIAM FSYTFGKVQG NSDLYWKAQR YRLIREFHSR PALAPPFIVI SHLRLLLRQL CRRPRSPQPS SPALEHFRVY LS KEAERKL LTWESVHKEN FLLARARDKR ESDSERLKRT SQKVDLALKQ LGHIREY

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration2.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4S4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), pH 7.4
150.0 mMNaClsodium chloride
5.0 mMC10H16N2O8Ethylenediaminetetraacetic acid (EDTA)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1817 / Average exposure time: 10.0 sec. / 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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500
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

DetailsK2 camera operating in super-resolution counting mode
Particle selectionNumber selected: 528648 / Details: Automatic picking
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: cryoSPARC ab initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 47242
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6bqr:
Human TRPM4 ion channel in lipid nanodiscs in a calcium-free state

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