9P3T | pdb_00009p3t

Zebrafish TRPM5 with 5mM calcium and 0.5mM TPPO

PDB DOI: https://doi.org/10.2210/pdb9P3T/pdb
EM Map EMD-71254: EMDB EMDataResource

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

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Ruan, Z., Du, J., Lu, W.

To be published.

Macromolecule Content

Total Structure Weight: 674.6 kDa
Atom Count: 30,780
Modeled Residue Count: 3,984
Deposited Residue Count: 5,900
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5	A, B, C, D	1,475	Danio rerio	Mutation(s): 0 Gene Names: GFP, trpm5
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for S5UH55 (Danio rerio) Explore S5UH55 Go to UniProtKB: S5UH55
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212S5UH55
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YUY Query on YUY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	H [auth A], N [auth B], T [auth C], Z [auth D]	(2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside C₄₄ H₇₂ O₁₅ DNENJNRTLMHVQJ-YVPDUETGSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
YUV Query on YUV Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C]	AA [auth D], I [auth A], O [auth B], U [auth C]	(25R)-14beta,17beta-spirost-5-en-3beta-ol C₂₇ H₄₂ O₃ WQLVFSAGQJTQCK-VKROHFNGSA-N		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]
A1CG5 (Subject of Investigation/LOI) Query on A1CG5 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain BA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain BA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain BA [auth D]	BA [auth D], J [auth A], P [auth B], V [auth C]	oxotri(phenyl)-lambda~5~-phosphane C₁₈ H₁₅ O P FIQMHBFVRAXMOP-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain V [auth C]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	E [auth A], K [auth B], Q [auth C], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain R [auth C] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain R [auth C] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain R [auth C] mmCIF format, chain F [auth A]	F [auth A] G [auth A] L [auth B] M [auth B] R [auth C] F [auth A], G [auth A], L [auth B], M [auth B], R [auth C], S [auth C], X [auth D], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-07

Deposition Author(s):

Ruan, Z.

Du, J.

Lu, W.

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