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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 channel
    • Protein or peptide: TRPM7
KeywordsCryoEM / Truncated mouse TRPM7 / MEMBRANE PROTEIN
Function / homology
Function and homology information


calcium-dependent cell-matrix adhesion / intracellular magnesium ion homeostasis / zinc ion transport / magnesium ion transmembrane transport / zinc ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / TRP channels / actomyosin structure organization / myosin binding / necroptotic process ...calcium-dependent cell-matrix adhesion / intracellular magnesium ion homeostasis / zinc ion transport / magnesium ion transmembrane transport / zinc ion transmembrane transporter activity / magnesium ion transmembrane transporter activity / TRP channels / actomyosin structure organization / myosin binding / necroptotic process / ruffle / cytoplasmic vesicle membrane / calcium channel activity / calcium ion transport / kinase activity / actin binding / protein autophosphorylation / cytoplasmic vesicle / protein homotetramerization / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / 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 / : ...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-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing 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
  • Imaged by UCSF Chimera
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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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å		1.23 Å/pix.
x 256 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
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 channel
Components
  • Cell: Membrane Protein, Transient Receptor Potential ion channel
    • 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
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

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

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