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- PDB-6bwf: 4.1 angstrom Mg2+-unbound structure of mouse TRPM7 -

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Basic information

Entry
Database: PDB / ID: 6bwf
Title4.1 angstrom Mg2+-unbound structure of mouse TRPM7
ComponentsTRPM7
KeywordsMEMBRANE PROTEIN / CryoEM / Truncated mouse TRPM7
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZhang, J. / Li, Z. / Duan, J. / Abiria, S.A. / 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
DepositionDec 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 15, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: TRPM7
B: TRPM7
C: TRPM7
D: TRPM7


Theoretical massNumber of molelcules
Total (without water)429,9024
Polymers429,9024
Non-polymers00
Water00
1


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

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Components

#1: Protein
TRPM7


Mass: 107475.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q923J1*PLUS
Has protein modificationN
Sequence detailsThe full sample sequence is MSQKSWIESTLTKRECVYIIPSSKDPHRCLPGCQICQQLVRCFCGRLVKQHACFTASLAMKYSDV ...The full sample sequence is MSQKSWIESTLTKRECVYIIPSSKDPHRCLPGCQICQQLVRCFCGRLVKQHACFTASLAMKYSDV KLGEHFNQAIEEWSVEKHTEQSPTDAYGVINFQGGSHSYRAKYVRLSYDTKPEIILQLLLKEWQM ELPKLVISVHGGMQKFELHPRIKQLLGKGLIKAAVTTGAWILTGGVNTGVAKHVGDALKEHASRS SRKICTIGIAPWGVIENRNDLVGRDVVAPYQTLLNPLSKLNVLNNLHSHFILVDDGTVGKYGAEV RLRRELEKTINQQRIHARIGQGVPVVALIFEGGPNVILTVLEYLQESPPVPVVVCEGTGRAADLL AYIHKQTEEGGNLPDAAEPDIISTIKKTFNFGQSEAVHLFQTMMECMKKKELITVFHIGSEDHQD IDVAILTALLKGTNASAFDQLILTLAWDRVDIAKNHVFVYGQQWLVGSLEQAMLDALVMDRVSFV KLLIENGVSMHKFLTIPRLEELYNTKQGPTNPMLFHLIRDVKQGNLPPGYKITLIDIGLVIEYLM GGTYRCTYTRKRFRLIYNSLGGNNRRSGRNTSSSTPQLRKSHETFGNRADKKEKMRHNHFIKTAQ PYRPKMDASMEEGKKKRTKDEIVDIDDPETKRFPYPLNELLIWACLMKRQVMARFLWQHGEESMA KALVACKIYRSMAYEAKQSDLVDDTSEELKQYSNDFGQLAVELLEQSFRQDETMAMKLLTYELKN WSNSTCLKLAVSSRLRPFVAHTCTQMLLSDMWMGRLNMRKNSWYKVILSILVPPAILMLEYKTKA EMSHIPQSQDAHQMTMEDSENNFHNITEEIPMEVFKEVKILDSSDGKNEMEIHIKSKKLPITRKF YAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAG KISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVR LLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHP YWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKA ISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKL HDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHL QDLSALTVDTLKTLTAQKASEASKVHNEITRELSISKHLAQNLIDDVPVRPLWKKPSAVNTLSSS

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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 channel
Type: CELL / Entity ID: all / 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 FIELD
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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206032 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00722738
ELECTRON MICROSCOPYf_angle_d1.40330896
ELECTRON MICROSCOPYf_dihedral_angle_d11.76513414
ELECTRON MICROSCOPYf_chiral_restr0.0633588
ELECTRON MICROSCOPYf_plane_restr0.0093915

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