9P3V | pdb_00009p3v

Zebrafish TRPM5 Q771A mutant with 5mM calcium and 0.5mM CBTA

• PDB DOI: https://doi.org/10.2210/pdb9P3V/pdb
• EM Map EMD-71256: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Danio rerio
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-06-14 Released: 2026-01-07 
• Deposition Author(s): Ruan, Z., Du, J., Lu, W.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A single allosteric site merges activation, modulation and inhibition in TRPM5.

Ruan, Z., Lee, J., Li, Y., Orozco, I.J., Du, J., Lu, W.

(2026) Nat Chem Biol 

• PubMed: 41491833 
• DOI: https://doi.org/10.1038/s41589-025-02097-7
• Primary Citation of Related Structures:  
  9P3N, 9P3O, 9P3P, 9P3Q, 9P3R, 9P3S, 9P3T, 9P3U, 9P3V, 9P3W


• PubMed Abstract: 
  

  TRPM5 is a Ca ²⁺ -activated monovalent cation channel essential for taste perception, insulin secretion and gastrointestinal chemosensation. Canonical TRPM5 activation requires Ca ²⁺ binding at two distinct sites: an agonist site within the lower vestibule of the S1-S4 pocket in the transmembrane domain (Ca _TMD ) and a modulatory site in the intracellular domain (Ca _ICD ) that tunes voltage dependence and agonist sensitivity. Here we characterize CBTA as a noncalcium agonist that binds to the upper vestibule of the S1-S4 pocket, directly above Ca _TMD . CBTA alone mimics the dual role of Ca _TMD and Ca _ICD , merging agonist activation with voltage modulation. CBTA also renders TRPM5 supersensitive to Ca ²⁺ , synergistically hyperactivating the channel even at near-resting Ca ²⁺ levels. We further demonstrate that the inhibitor triphenylphosphine oxide binds the same site but stabilizes a nonconductive state. These opposing effects reveal the upper S1-S4 pocket as a multifunctional regulatory hub integrating activation, inhibition and modulation in TRPM5.

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Organizational Affiliation: 
• Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
Department of Biochemistry & Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
AnaBios Corporation, San Diego, CA, USA.
Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA. [e-mail].
Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. [e-mail].
Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. [e-mail].
Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. [e-mail].
Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA. [e-mail].
Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. [e-mail].
Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA. [e-mail].
Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 674.54 kDa 
• Atom Count: 30,656 
• Modeled Residue Count: 3,984 
• Deposited Residue Count: 5,900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5	A, B, C, D	1,475	Danio rerio	Mutation(s): 1  EC: 2.1.1.375 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 2.7.7.88 (PDB Primary Data)
UniProt
Find proteins for A0A5P9VSM8 (Human respiratory syncytial virus) Explore A0A5P9VSM8  Go to UniProtKB:  A0A5P9VSM8
Find proteins for S5UH55 (Danio rerio) Explore S5UH55  Go to UniProtKB:  S5UH55
UniProt Groups	S5UH55A0A5P9VSM8
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CG0	J [auth A], P [auth B], V [auth C], W [auth D]	(2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside C44 H74 O15 WVVNJMRPVIVJJT-WHGCCSAPSA-N
A1CGZ	AA [auth D], H [auth A], N [auth B], T [auth C]	Tigogenin C27 H44 O3 GMBQZIIUCVWOCD-MFRNJXNGSA-N
A1CGW (Subject of Investigation/LOI)	BA [auth D], I [auth A], O [auth B], U [auth C]	5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine C11 H7 Cl2 N3 S2 GFNMKESSHVFPQM-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	E [auth A], K [auth B], Q [auth C], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)	F [auth A], G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], Y [auth D], Z [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-07 
Deposition Author(s): Ruan, Z., Du, J., Lu, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R00NS128258
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL153219
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS112363
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM138321
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS111031
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS129804

Revision History  

• Version 1.0: 2026-01-07
  Type: Initial release
  
• Version 1.1: 2026-01-21
  Changes: Data collection, Database references, Derived calculations, Structure summary