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- PDB-9vqw: Cryo-EM structure of drosophila TRPgamma determined in GDN, state 2 -

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Basic information

Entry
Database: PDB / ID: 9vqw
TitleCryo-EM structure of drosophila TRPgamma determined in GDN, state 2
ComponentsTransient receptor potential-gamma protein
KeywordsMEMBRANE PROTEIN / Transient receptor potential cation channel gamma
Function / homology
Function and homology information


Ion homeostasis / rhabdomere membrane / TRP channels / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / rhabdomere / neuromuscular process controlling posture / store-operated calcium channel activity / detection of light stimulus involved in visual perception / proximal dendrite / mechanosensitive monoatomic ion channel activity ...Ion homeostasis / rhabdomere membrane / TRP channels / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / rhabdomere / neuromuscular process controlling posture / store-operated calcium channel activity / detection of light stimulus involved in visual perception / proximal dendrite / mechanosensitive monoatomic ion channel activity / cation channel complex / inositol 1,4,5 trisphosphate binding / adult walking behavior / response to light stimulus / monoatomic cation transport / regulation of cytosolic calcium ion concentration / monoatomic cation channel activity / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / neuronal cell body / plasma membrane
Similarity search - Function
: / Calcium channel YVC1-like, C-terminal / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. ...: / Calcium channel YVC1-like, C-terminal / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-POV / Chem-PT5 / CHOLESTEROL HEMISUCCINATE / Chem-YZY / Transient receptor potential-gamma protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsPang, P. / Yao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371200 China
CitationJournal: To Be Published
Title: Chemoreceptor TRPgamma coordinates locomotor activity via regulating intracellular Ca2+ homeostasis in Drosophila
Authors: Pang, P. / Gao, B. / Mo, X. / Lu, X. / Wang, P. / Li, X. / Shi, Q. / Xia, K. / Gai, H. / Xie, C. / Li, D. / Sun, D. / Tian, C. / Yao, J.
History
DepositionJul 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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: Transient receptor potential-gamma protein
B: Transient receptor potential-gamma protein
C: Transient receptor potential-gamma protein
D: Transient receptor potential-gamma protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,01728
Polymers509,0394
Non-polymers11,97724
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Transient receptor potential-gamma protein / TRPgamma / Transient receptor potential cation channel gamma


Mass: 127259.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Trpgamma, CG5996 / Production host: Homo sapiens (human) / References: UniProt: Q9VJJ7

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Non-polymers , 7 types, 44 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-YZY / (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate


Mass: 594.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H70O5
#5: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#6: Chemical
ChemComp-PT5 / [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol 4,5-bisphosphate / PtdIns(4,5)P2


Mass: 1047.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H85O19P3 / Comment: phospholipid*YM
#7: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: transient receptor potential cation channel gamma / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.2
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 defocus max: -2400 nm / Nominal defocus min: -1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148474 / Symmetry type: POINT

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