6PUO

Human TRPM2 in the apo state

• PDB DOI: https://doi.org/10.2210/pdb6PUO/pdb
• EM Map EMD-20478: EMDB EMDataResource

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


• Deposited: 2019-07-18 Released: 2019-09-25 
• Deposition Author(s): Du, J., Lu, W., Huang, Y.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel.

Huang, Y., Roth, B., Lu, W., Du, J.

(2019) Elife 8

• PubMed: 31513012 
• DOI: https://doi.org/10.7554/eLife.50175
• Primary Citation of Related Structures:  
  6PUO, 6PUR, 6PUS, 6PUU


• PubMed Abstract: 
  

  TRPM2 is critically involved in diverse physiological processes including core temperature sensing, apoptosis, and immune response. TRPM2's activation by Ca ²⁺ and ADP ribose (ADPR), an NAD ⁺ -metabolite produced under oxidative stress and neurodegenerative conditions, suggests a role in neurological disorders. We provide a central concept between triple-site ligand binding and the channel gating of human TRPM2. We show consecutive structural rearrangements and channel activation of TRPM2 induced by binding of ADPR in two indispensable locations, and the binding of Ca ²⁺ in the transmembrane domain. The 8-Br-cADPR-an antagonist of cADPR-binds only to the MHR1/2 domain and inhibits TRPM2 by stabilizing the channel in an apo-like conformation. We conclude that MHR1/2 acts as a orthostatic ligand-binding site for TRPM2. The NUDT9-H domain binds to a second ADPR to assist channel activation in vertebrates, but not necessary in invertebrates. Our work provides insights into the gating mechanism of human TRPM2 and its pharmacology.

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Organizational Affiliation: 

Van Andel Institute, Grand Rapids, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 689.12 kDa 
• Atom Count: 37,804 
• Modelled Residue Count: 5,208 
• Deposited Residue Count: 6,048 
• 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, C, D	1,512	Homo sapiens	Mutation(s): 0  Gene Names: TRPM2, EREG1, KNP3, LTRPC2, TRPC7 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O94759 (Homo sapiens) Explore O94759  Go to UniProtKB:  O94759
PHAROS:  O94759 GTEx:  ENSG00000142185

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Du, J., Lu, W., Huang, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS111031

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references