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- EMDB-65280: Cryo-EM structure of drosophila TRPgamma, calcium free, state 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-65280
TitleCryo-EM structure of drosophila TRPgamma, calcium free, state 2
Map data
Sample
  • Complex: transient receptor potential cation channel gamma
    • Protein or peptide: Transient receptor potential-gamma protein
  • Ligand: ZINC ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(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
  • Ligand: water
KeywordsTransient receptor potential cation channel gamma / MEMBRANE PROTEIN
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
Transient receptor potential-gamma protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsPang P / Yao J
Funding support China, 1 items
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, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65280.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å		0.82 Å/pix.
x 384 pix.
= 316.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.75629675 - 1.3623142
Average (Standard dev.)0.00014575942 (±0.03492815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65280_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65280_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : transient receptor potential cation channel gamma

EntireName: transient receptor potential cation channel gamma
Components
  • Complex: transient receptor potential cation channel gamma
    • Protein or peptide: Transient receptor potential-gamma protein
  • Ligand: ZINC ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: [(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
  • Ligand: water

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Supramolecule #1: transient receptor potential cation channel gamma

SupramoleculeName: transient receptor potential cation channel gamma / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Transient receptor potential-gamma protein

MacromoleculeName: Transient receptor potential-gamma protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 127.259867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMEEENTIRP HQEIRQLTLE EKKFLLAVER GDMAGTRRML QKAQDTEYIN VNCVDPLGRT ALLMAIDNEN LEMVELLINY NVDTKDALL HSISEEFVEA VEVLLDHENV TFHSEGNHSW ESASEDTSTF TPDITPLILA AHRDNYEIIK ILLDRGAVLP M PHDVRCGC ...String:
MMEEENTIRP HQEIRQLTLE EKKFLLAVER GDMAGTRRML QKAQDTEYIN VNCVDPLGRT ALLMAIDNEN LEMVELLINY NVDTKDALL HSISEEFVEA VEVLLDHENV TFHSEGNHSW ESASEDTSTF TPDITPLILA AHRDNYEIIK ILLDRGAVLP M PHDVRCGC DECVQSRQED SLRHSRSRIN AYRALASPSL IALSSKDPIL TAFELSWELR RLSFLEHEFK NEYQELRKQC QD FATALLD HTRTSHELEI LLNHDPTGPV YEHGERMHLN RLKLAIKLRQ KKFVAHSNVQ QLLASIWYEG LPGFRRKNMA LQA VDIIRI GIMFPIFSLA YILAPYSSIG QTMRKPFIKF ICHSASYFTF LFLLMLASQR IETFIGGWFF ADSSGMLNTM EELP TKRGA KPTFIEWLIL AWVSGLIWSE VKQLWDVGLQ EYLNDMWNVI DFVTNSLYVA TVALRVVSFF QVQKEMIYNS HATDL PRER WDAWDPMLIS EGLFSAANIF SSLKLVYIFS VNPHLGPLQV SLSRMVMDIM KFFFLYVLVL FAFGSGLNQL LWYYAD LEK KRCPEVSPMS ALLNMNGTND PNACIVWRRF SNLFETTQTL FWAVFGLIDL DSFELDGIKI FTRFWGMLMF GTYSVIN IV VLLNLLIAMM NHSYQLISER ADVEWKFARS KLWISYFEEG GTCPPPFNII PTPKSIWYAI KWMRRVFCSG SSAARREH L KTIRRKAQQA SDRDFKYQQI MRNLVRRYVT VEQRKAESQG VTEDDVNEIK QDISAFRCEL VEILKNSGMD TNVTAGQGG GGGGKKNRQK ERRLMKGFNI APPGSTGSLA PVAEFSTSLD NYDNQHEILS STLSTLFTPN FMHKRQQSQA GSGGGGSESP TTPTAPQGT QGAAMTASSQ VTKYNKSALK PYNKRIAGHK KRWGTLIEAA KVGNVSKMLG RSKSEDSVCN SSHTSTPVHG Q MRVTYAQN SPQQEYGYHG ETSSTTISTP TPTISVVSNS PAAHAGVGSH FFHTTSGLTA IAALKRKRKK FSSSKNICPV TE SVAAANA AEILNDKTLK RVSSYPAAEA GVQHNPAQLV KPRRHEQTQS QHDSVETNST FTLSIDPSNT SVNSREPLIS TSC VSTTGA IG

UniProtKB: Transient receptor potential-gamma protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #4: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 4 / Formula: YZY
Molecular weightTheoretical: 594.949 Da
Chemical component information

ChemComp-YZY:
(2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tr...

MacromoleculeName: [(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
type: ligand / ID: 6 / Number of copies: 4 / Formula: PT5
Molecular weightTheoretical: 1.047088 KDa

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.5 µm / Nominal defocus min: -1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 84557
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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