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- PDB-9p3n: The open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA -

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Basic information

Entry
Database: PDB / ID: 9p3n
TitleThe open state of zebrafish TRPM5 with 1mM EDTA and 0.5mM CBTA
ComponentsGreen fluorescent protein,Transient receptor potential cation channel subfamily M member 5
KeywordsTRANSPORT PROTEIN / TRPM5 channel / ion channel / cation channel / sodium channel / calcium / CBTA
Function / homology
Function and homology information


calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / calcium channel activity / calcium ion binding / identical protein binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical / TRPM, SLOG domain / : / SLOG in TRPM / TRPM2-like domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / (25R)-14beta,17beta-spirost-5-en-3beta-ol / Chem-YUY / Green fluorescent protein / Transient receptor potential cation channel subfamily M member 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRuan, Z. / Du, J. / Lu, W.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R00NS128258 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL153219 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS112363 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138321 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS111031 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS129804 United States
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: A single allosteric site merges activation, modulation and inhibition in TRPM5
Authors: Ruan, Z. / Du, J. / Lu, W.
History
DepositionJun 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 7, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
D: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
B: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
C: Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)673,71120
Polymers667,2634
Non-polymers6,44816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Green fluorescent protein,Transient receptor potential cation channel subfamily M member 5


Mass: 166815.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: GFP, trpm5 / Production host: Homo sapiens (human) / References: UniProt: P42212, UniProt: S5UH55
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-YUY / (2R)-2-(hydroxymethyl)-4-{[(25R)-10alpha,14beta,17beta-spirost-5-en-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 841.033 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H72O15
#4: Chemical
ChemComp-YUV / (25R)-14beta,17beta-spirost-5-en-3beta-ol


Mass: 414.621 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H42O3
#5: Chemical
ChemComp-A1CGW / 5-chloro-N-[(5-chloro-1,3-thiazol-2-yl)methyl]-1,2-benzothiazol-6-amine


Mass: 316.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H7Cl2N3S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Open state of zebrafish TRPM5 in GDN detergent with 1mM EDTA and 0.5mM CBTA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Danio rerio (zebrafish)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5426 / Symmetry type: POINT

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