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- PDB-9p3w: Zebrafish TRPM5 Q771A mutant with 5mM calcium -

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Basic information

Entry
Database: PDB / ID: 9p3w
TitleZebrafish TRPM5 Q771A mutant with 5mM calcium
ComponentsRNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
KeywordsTRANSFERASE / TRPM5 channel / ion channel / cation channel / sodium channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / virion component / calcium channel activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity ...NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / calcium-activated cation channel activity / bioluminescence / generation of precursor metabolites and energy / virion component / calcium channel activity / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / calcium ion binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Transient receptor potential channel, canonical / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase ...RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Transient receptor potential channel, canonical / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / 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
: / : / RNA-directed RNA polymerase L / Transient receptor potential cation channel subfamily M member 5
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 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: To Be Published
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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
B: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
C: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
D: RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)673,27924
Polymers667,0354
Non-polymers6,24420
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
RNA-directed RNA polymerase L,Transient receptor potential cation channel subfamily M member 5 / Large structural protein / Replicase / Transcriptase


Mass: 166758.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trpm5 / Production host: Homo sapiens (human)
References: UniProt: A0A5P9VSM8, UniProt: S5UH55, NNS virus cap methyltransferase, RNA-directed RNA polymerase, GDP polyribonucleotidyltransferase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-A1CGZ / (10xi,22xi,25R)-5beta,13xi,14beta,17beta-spirostan-3beta-ol


Mass: 416.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H44O3
#5: Chemical
ChemComp-A1CG0 / (2R)-2-(hydroxymethyl)-4-{[(10xi,13xi,22xi,25R)-5beta,14beta,17beta-spirostan-3beta-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 843.049 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H74O15
Has ligand of interestY
Has protein modificationY

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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: zebrafish TRPM5 D797A mutant in GDN detergent with 5mM calcium
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: 300 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

EM software
IDNameVersionCategory
1RELIONparticle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3662754 / Symmetry type: POINT
RefinementHighest resolution: 2.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00331380
ELECTRON MICROSCOPYf_angle_d0.56142908
ELECTRON MICROSCOPYf_dihedral_angle_d4.8364620
ELECTRON MICROSCOPYf_chiral_restr0.0395140
ELECTRON MICROSCOPYf_plane_restr0.0055224

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