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- PDB-9opu: Structure of a constitutively open human TRPC3 mutant -

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Basic information

Entry
Database: PDB / ID: 9opu
TitleStructure of a constitutively open human TRPC3 mutant
ComponentsShort transient receptor potential channel 3
KeywordsMEMBRANE PROTEIN / TRPC3 / cerebellar ataxia / moonwalker
Function / homology
Function and homology information


Role of second messengers in netrin-1 signaling / positive regulation of cardiac muscle hypertrophy in response to stress / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium-activated cation channel activity / TRP channels / response to ATP ...Role of second messengers in netrin-1 signaling / positive regulation of cardiac muscle hypertrophy in response to stress / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / cation channel complex / calcium-activated cation channel activity / TRP channels / response to ATP / positive regulation of calcium ion transport into cytosol / phototransduction / single fertilization / regulation of cytosolic calcium ion concentration / MECP2 regulates neuronal receptors and channels / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Unknown ligand / Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBell, B. / Baker, M.L. / Cordero-Morales, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149218 United States
CitationJournal: To Be Published
Title: Functional and Structural Basis of a Hypermorphic TRPC3 variant
Authors: Bell, B. / Jaramillo-Granada, A.M. / Romero, L.O. / Gutierrez, I.A. / Mallampalli, V.K.P.S. / Fan, G. / Varma, S. / Baker, M.L. / Serysheva, I.I. / Vasquez, V. / Cordero-Morales, J.F.
History
DepositionMay 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short transient receptor potential channel 3
B: Short transient receptor potential channel 3
C: Short transient receptor potential channel 3
D: Short transient receptor potential channel 3


Theoretical massNumber of molelcules
Total (without water)376,61316
Polymers376,6134
Non-polymers012
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
Short transient receptor potential channel 3 / TrpC3 / Transient receptor protein 3 / TRP-3 / hTrp-3 / hTrp3


Mass: 94153.156 Da / Num. of mol.: 4 / Mutation: T573A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC3, TRP3 / Production host: Homo sapiens (human) / References: UniProt: Q13507
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 12 / Source method: obtained synthetically
Has ligand of interestN
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: T573A/Delta 28 mutant human TRPC3 tetrameric complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22373 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7DXD

7dxd


Accession code: 7DXD / Details: Used for refinement into the map / Source name: PDB / Type: experimental model

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