6D73 | pdb_00006d73

Cryo-EM structure of the zebrafish TRPM2 channel in the presence of Ca2+

• PDB DOI: https://doi.org/10.2210/pdb6D73/pdb
• EM Map EMD-7822: EMDB EMDataResource

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


• Deposited: 2018-04-23 Released: 2019-05-15 
• Deposition Author(s): Yin, Y., Wu, M., Borschel, W.F., Lander, G.C., Lee, S.-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: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel.

Yin, Y., Wu, M., Hsu, A.L., Borschel, W.F., Borgnia, M.J., Lander, G.C., Lee, S.Y.

(2019) Nat Commun 10: 3740-3740

• PubMed: 31431622 
• DOI: https://doi.org/10.1038/s41467-019-11733-5
• Primary Citation Related Structures: 
  6D73, 6PKV, 6PKW, 6PKX


• PubMed Abstract: 
  

  The transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types. Channel activation requires binding of both ADP-ribose (ADPR) and Ca ²⁺ . The recently published TRPM2 structures from Danio rerio in the ligand-free and the ADPR/Ca ²⁺ -bound conditions represent the channel in closed and open states, which uncovered substantial tertiary and quaternary conformational rearrangements. However, it is unclear how these rearrangements are achieved within the tetrameric channel during channel gating. Here we report the cryo-electron microscopy structures of Danio rerio TRPM2 in the absence of ligands, in complex with Ca ²⁺ alone, and with both ADPR and Ca ²⁺ , resolved to ~4.3 Å, ~3.8 Å, and ~4.2 Å, respectively. In contrast to the published results, our studies capture ligand-bound TRPM2 structures in two-fold symmetric intermediate states, offering a glimpse of the structural transitions that bridge the closed and open conformations.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA.
Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (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: 670.59 kDa 
• Atom Count: 35,340 
• Modeled Residue Count: 4,966 
• Deposited Residue Count: 5,864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel, subfamily M	A [auth B], B [auth A], C, D	1,466	Danio rerio	Mutation(s): 0  Gene Names: trpm2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth B], F [auth A], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.12-2829-000
MODEL REFINEMENT	Coot	0.8.8

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Yin, Y., Wu, M., Borschel, W.F., Lander, G.C., Lee, S.-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	--

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Structure summary
• Version 1.2: 2019-11-27
  Changes: Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary