6DRK | pdb_00006drk

Structure of TRPM2 ion channel receptor by single particle electron cryo-microscopy, Apo state

• PDB DOI: https://doi.org/10.2210/pdb6DRK/pdb
• EM Map EMD-8901: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Danio rerio
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-06-12 Released: 2018-09-19 
• Deposition Author(s): Du, J., Lu, W., Huang, Y., Winkler, P., Sun, W.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium.

Huang, Y., Winkler, P.A., Sun, W., Lu, W., Du, J.

(2018) Nature 562: 145-149

• PubMed: 30250252 
• DOI: https://doi.org/10.1038/s41586-018-0558-4
• Primary Citation Related Structures: 
  6DRJ, 6DRK


• PubMed Abstract: 
  

  Transient receptor potential melastatin 2 (TRPM2) is a calcium-permeable, non-selective cation channel that has an essential role in diverse physiological processes such as core body temperature regulation, immune response and apoptosis ^1-4 . TRPM2 is polymodal and can be activated by a wide range of stimuli ^1-7 , including temperature, oxidative stress and NAD ⁺ -related metabolites such as ADP-ribose (ADPR). Its activation results in both Ca ²⁺ entry across the plasma membrane and Ca ²⁺ release from lysosomes ⁸ , and has been linked to diseases such as ischaemia-reperfusion injury, bipolar disorder and Alzheimer's disease ^9-11 . Here we report the cryo-electron microscopy structures of the zebrafish TRPM2 in the apo resting (closed) state and in the ADPR/Ca ²⁺ -bound active (open) state, in which the characteristic NUDT9-H domains hang underneath the MHR1/2 domain. We identify an ADPR-binding site located in the bi-lobed structure of the MHR1/2 domain. Our results provide an insight into the mechanism of activation of the TRPM channel family and define a framework for the development of therapeutic agents to treat neurodegenerative diseases and temperature-related pathological conditions.

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Organizational Affiliation: 
• Van Andel Research Institute, Grand Rapids, MI, USA.
Vollum Institute, Oregon Health & Science University, Portland, OR, USA.
Janelia Research Campus, Ashburn, VA, USA.
Van Andel Research Institute, Grand Rapids, MI, USA. [e-mail].
Van Andel Research Institute, Grand Rapids, MI, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 674.92 kDa 
• Atom Count: 33,120 
• Modeled Residue Count: 5,060 
• Deposited Residue Count: 5,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel, subfamily M, member 2	A, B [auth C], C [auth B], D	1,474	Danio rerio	Mutation(s): 0  Gene Names: trpm2 Membrane Entity: Yes
UniProt
Find proteins for A0A0R4IMY7 (Danio rerio) Explore A0A0R4IMY7  Go to UniProtKB:  A0A0R4IMY7

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Du, J., Lu, W., Huang, Y., Winkler, P., Sun, W.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-09-26
  Changes: Data collection, Structure summary
• Version 1.2: 2018-10-10
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2025-05-14
  Changes: Data collection