5ZX5 | pdb_00005zx5

3.3 angstrom structure of mouse TRPM7 with EDTA

PDB DOI: https://doi.org/10.2210/pdb5ZX5/pdb
EM Map EMD-6975: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2018-05-18 Released: 2018-10-17
Deposition Author(s): Zhang, J., Li, Z., Duan, J., Li, J., Hulse, R.E., Santa-Cruz, A., Abiria, S.A., Krapivinsky, G., Clapham, D.E.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.28 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the mammalian TRPM7, a magnesium channel required during embryonic development.

Duan, J., Li, Z., Li, J., Hulse, R.E., Santa-Cruz, A., Valinsky, W.C., Abiria, S.A., Krapivinsky, G., Zhang, J., Clapham, D.E.

(2018) Proc Natl Acad Sci U S A 115: E8201-E8210

PubMed: 30108148 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1810719115
Primary Citation Related Structures:
5ZX5, 6BWD, 6BWF

PubMed 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 and an α-kinase. The channel domain comprises a nonselective cation channel with notable permeability to Mg ²⁺ and Zn ²⁺ 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 ²⁺ ions occupying the center of the conduction pore. In high [Mg ²⁺], 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.

Organizational Affiliation

Department of Cardiology, Boston Children's Hospital, Boston, MA 02115.

Macromolecule Content

Total Structure Weight: 571.51 kDa
Atom Count: 25,440
Modeled Residue Count: 3,256
Deposited Residue Count: 4,916
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily M member 7	A, B, C, D	1,229	Mus musculus	Mutation(s): 0 Gene Names: Trpm7, Chak, Ltrpc7 EC: 2.7.11.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q923J1 (Mus musculus) Explore Q923J1 Go to UniProtKB: Q923J1
IMPC: MGI:1929996
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q923J1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]