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- EMDB-7298: 4.1 angstrom Mg2+-unbound structure of mouse TRPM7 -

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Basic information

Entry
Database: EMDB / ID: EMD-7298
Title4.1 angstrom Mg2+-unbound structure of mouse TRPM7
Map data
Sample
  • Cell: Membrane Protein, Transient Receptor Potential ion channelBiological membrane
    • Protein or peptide: TRPM7
KeywordsCryoEM / Truncated mouse TRPM7 / MEMBRANE PROTEIN
Function / homology
Function and homology information


intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle ...intracellular magnesium ion homeostasis / calcium-dependent cell-matrix adhesion / varicosity / TRP channels / actomyosin structure organization / myosin binding / monoatomic cation transmembrane transport / necroptotic process / monoatomic cation channel activity / ruffle / protein tetramerization / calcium channel activity / synaptic vesicle membrane / memory / calcium ion transport / actin binding / kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of apoptotic process / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / SLOG in TRPM ...Transient receptor potential cation channel subfamily M member 7 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / TRPM, tetramerisation domain / TRPM, tetramerisation domain superfamily / Tetramerisation domain of TRPM / TRPM, SLOG domain / SLOG in TRPM / Ion transport domain / Ion transport protein / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily M member 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhang J / Li Z
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure of the mammalian TRPM7, a magnesium channel required during embryonic development.
Authors: Jingjing Duan / Zongli Li / Jian Li / Raymond E Hulse / Ana Santa-Cruz / William C Valinsky / Sunday A Abiria / Grigory Krapivinsky / Jin Zhang / David E Clapham /
Abstract: The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel ...The transient receptor potential ion channel subfamily M, member 7 (TRPM7), is a ubiquitously expressed protein that is required for mouse embryonic development. TRPM7 contains both an ion channel and an α-kinase. The channel domain comprises a nonselective cation channel with notable permeability to Mg and Zn Here, we report the closed state structures of the mouse TRPM7 channel domain in three different ionic conditions to overall resolutions of 3.3, 3.7, and 4.1 Å. The structures reveal key residues for an ion binding site in the selectivity filter, with proposed partially hydrated Mg ions occupying the center of the conduction pore. In high [Mg], a prominent external disulfide bond is found in the pore helix, which is essential for ion channel function. Our results provide a structural framework for understanding the TRPM1/3/6/7 subfamily and extend the knowledge base upon which to study the diversity and evolution of TRP channels.
History
DepositionDec 14, 2017-
Header (metadata) releaseJul 18, 2018-
Map releaseAug 15, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6bwf
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bwf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7298.png

Downloads & links

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Map

FileDownload / File: emd_7298.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy EMDB: 0.0227 / Movie #1: 0.02
Minimum - Maximum-0.091829 - 0.13612443
Average (Standard dev.)0.0002027354 (±0.0035939107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0920.1360.000

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Supplemental data

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Sample components

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Entire : Membrane Protein, Transient Receptor Potential ion channel

EntireName: Membrane Protein, Transient Receptor Potential ion channelBiological membrane
Components
  • Cell: Membrane Protein, Transient Receptor Potential ion channelBiological membrane
    • Protein or peptide: TRPM7

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Supramolecule #1: Membrane Protein, Transient Receptor Potential ion channel

SupramoleculeName: Membrane Protein, Transient Receptor Potential ion channel
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: TRPM7

MacromoleculeName: TRPM7 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 107.475609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)KFL TIPRLEELYN TKQGPTNPML FHLIRDVKQG NLPPGYK IT LIDIGLVIEY LMGGTYRCTY TRKRFRLIYN SLGGNNRRSG RNTSSSTPQL RKSHETFGNR ADKKEKMRHN HFIKTAQP Y RPKMDASMEE GKKKRTKDEI VDIDDPETKR FPYPLNELLI WACLMKRQVM ARFLWQHGEE SMAKALVACK IYRSMAYEA KQSDLVDDTS EELKQYSNDF GQLAVELLEQ SFRQDETMAM KLLTYELKNW SNSTCLKLAV SSRLRPFVAH TCTQMLLSDM WMGRLNMRK NSWYKVILSI LVPPAILMLE YKTKAEMSHI PQSQDAHQMT MEDSENNFHN ITEEIPMEVF KEVKILDSSD G KNEMEIHI KSKKLPITRK FYAFYHAPIV KFWFNTLAYL GFLMLYTFVV LVKMEQLPSV QEWIVIAYIF TYAIEKVREV FM SEAGKIS QKIKVWFSDY FNVSDTIAII SFFVGFGLRF GAKWNYINAY DNHVFVAGRL IYCLNIIFWY VRLLDFLAVN QQA GPYVMM IGKMVANMFY IVVIMALVLL SFGVPRKAIL YPHEEPSWSL AKDIVFHPYW MIFGEVYAYE IDVCANDSTL PTIC GPGTW LTPFLQAVYL FVQYIIMVNL LIAFFNNVYL QVKAISNIVW KYQRYHFIMA YHEKPVLPPP LIILSHIVSL FCCVC KRRK KDKTSDGPKL FLTEEDQKKL HDFEEQCVEM YFDEKDDKFN SGSEERIRVT FERVEQMSIQ IKEVGDRVNY IKRSLQ SLD SQIGHLQDLS ALTVDTLKTL TAQKASEASK VHNEITRELS ISKHLAQNLI DDVPVRPLWK KPSAVNTLSS S

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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 / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI POLARA 300
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 BASE (4k x 4k) / Average electron dose: 56.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206032

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