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- PDB-5zx5: 3.3 angstrom structure of mouse TRPM7 with EDTA -

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Basic information

Entry
Database: PDB / ID: 5zx5
Title3.3 angstrom structure of mouse TRPM7 with EDTA
ComponentsTransient receptor potential cation channel subfamily M member 7
KeywordsTRANSFERASE / CryoEM / 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
CHOLESTEROL HEMISUCCINATE / Transient receptor potential cation channel subfamily M member 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZhang, J. / Li, Z. / Duan, J. / Li, J. / Hulse, R.E. / Santa-Cruz, A. / Abiria, S.A. / Krapivinsky, G. / Clapham, D.E.
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
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily M member 7
B: Transient receptor potential cation channel subfamily M member 7
C: Transient receptor potential cation channel subfamily M member 7
D: Transient receptor potential cation channel subfamily M member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)571,51216
Polymers565,6714
Non-polymers5,84112
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Transient receptor potential cation channel subfamily M member 7 / Channel-kinase 1 / Long transient receptor potential channel 7 / LTrpC7 / Transient receptor ...Channel-kinase 1 / Long transient receptor potential channel 7 / LTrpC7 / Transient receptor potential-phospholipase C-interacting kinase / TRP-PLIK


Mass: 141417.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpm7, Chak, Ltrpc7 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q923J1, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C31H50O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Membrane Protein, Transient Receptor Potential ion channelBiological membrane
Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
Image processingDetails: TRPM7 image stacks were recorded on Gatan K2 Summit (Gatan) direct detector set in super-resolution counting mode using SerialEM
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2068004
Details: Particle picking and subsequent bad particle elimination through 2D classification was performed using Python scripts/programs developed by Maofu Liao (Ru et al., 2015) with minor ...Details: Particle picking and subsequent bad particle elimination through 2D classification was performed using Python scripts/programs developed by Maofu Liao (Ru et al., 2015) with minor modifications in the 8x binned images.
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1039775 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01626032
ELECTRON MICROSCOPYf_angle_d1.46935440
ELECTRON MICROSCOPYf_dihedral_angle_d12.46216008
ELECTRON MICROSCOPYf_chiral_restr0.1484196
ELECTRON MICROSCOPYf_plane_restr0.0084328

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