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- EMDB-33895: Structure of TRPA1 in Drosophila melanogaster in a state with 17 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33895
TitleStructure of TRPA1 in Drosophila melanogaster in a state with 17 ankyrin repeats determined
Map data
Sample
  • Complex: Homotetramer of dTRPA1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1
Keywordsion channel / TRPA1 / MEMBRANE PROTEIN
Function / homology
Function and homology information


temperature compensation of the circadian clock / negative phototaxis / TRP channels / neuronal signal transduction / thermosensory behavior / temperature-gated cation channel activity / mechanosensory behavior / detection of chemical stimulus involved in sensory perception of bitter taste / cation channel complex / detection of chemical stimulus involved in sensory perception of pain ...temperature compensation of the circadian clock / negative phototaxis / TRP channels / neuronal signal transduction / thermosensory behavior / temperature-gated cation channel activity / mechanosensory behavior / detection of chemical stimulus involved in sensory perception of bitter taste / cation channel complex / detection of chemical stimulus involved in sensory perception of pain / thermotaxis / detection of temperature stimulus involved in thermoception / detection of temperature stimulus involved in sensory perception of pain / monoatomic cation transport / ligand-gated monoatomic ion channel activity / phototransduction / response to light stimulus / positive regulation of calcium-mediated signaling / monoatomic cation channel activity / calcium channel activity / calcium ion transport / cellular response to heat / response to heat / membrane / plasma membrane
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Transient receptor potential cation channel subfamily A member 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun L / Liu X / Yang Z / Wang X
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022029 China
Other government2008085J15, 2008085MC90
Other governmentYD9100002004
Ministry of Science and Technology (MoST, China)20211890004 China
CitationJournal: Cell Discov / Year: 2023
Title: Molecular architecture and gating mechanisms of the Drosophila TRPA1 channel.
Authors: Xiaofei Wang / Yawen Li / Hong Wei / Zhisen Yang / Rui Luo / Yongxiang Gao / Wei Zhang / Xin Liu / Linfeng Sun /
Abstract: The transient receptor potential channel subfamily A member 1 (TRPA1) ion channel is an evolutionary conserved polymodal sensor responding to noxious temperature or chemical stimuli. Notably, the ...The transient receptor potential channel subfamily A member 1 (TRPA1) ion channel is an evolutionary conserved polymodal sensor responding to noxious temperature or chemical stimuli. Notably, the thermosensitivity of TRPA1 varies among different species or even different isoforms in the same species. However, the underlying molecular basis of its thermo-gating remains largely unknown. Here, we determine the structures of a heat-sensitive isoform of TRPA1 in Drosophila melanogaster in two distinct conformations with cryo-samples prepared at 8 °C. Large conformational changes are observed in the ankyrin repeat domain (ARD) and the coiled-coil domain between the two states. Remarkably, all 17 ankyrin repeats are mapped in the newly resolved conformation, forming a propeller-like architecture. Two intersubunit interfaces are identified in the amino (N)-terminal domain, and play vital roles during both heat and chemical activation as shown by electrophysiological analysis. With cryo-samples prepared at 35 °C, only one conformation is resolved, suggesting possible state transitions during heat responses. These findings provide a basis for further understanding how the ARD regulates channel functions, and insights into the gating mechanism of TRPA1.
History
DepositionJul 23, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33895.png

Downloads & links

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Map

FileDownload / File: emd_33895.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.645381 - 2.6683588
Average (Standard dev.)0.0059764097 (±0.10232455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 258.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33895_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_33895_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer of dTRPA1

EntireName: Homotetramer of dTRPA1
Components
  • Complex: Homotetramer of dTRPA1
    • Protein or peptide: Transient receptor potential cation channel subfamily A member 1

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Supramolecule #1: Homotetramer of dTRPA1

SupramoleculeName: Homotetramer of dTRPA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Transient receptor potential cation channel subfamily A member 1

MacromoleculeName: Transient receptor potential cation channel subfamily A member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 135.324359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSGDKETPK REDFASALRF LMGGCAREPE MTAMAPLNLP KKWARILRMS STPKIPIVDY LEAAESGNLD DFKRLFMADN SRIALKDAK GRTAAHQAAA RNRVNILRYI RDQNGDFNAK DNAGNTPLHI AVESDAYDAL DYLLSIPVDT GVLNEKKQAP V HLATELNK ...String:
MTSGDKETPK REDFASALRF LMGGCAREPE MTAMAPLNLP KKWARILRMS STPKIPIVDY LEAAESGNLD DFKRLFMADN SRIALKDAK GRTAAHQAAA RNRVNILRYI RDQNGDFNAK DNAGNTPLHI AVESDAYDAL DYLLSIPVDT GVLNEKKQAP V HLATELNK VKSLRVMGQY RNVIDIQQGG EHGRTALHLA AIYDHEECAR ILITEFDACP RKPCNNGYYP IHEAAKNASS KT MEVFFQW GEQRGCTREE MISFYDSEGN VPLHSAVHGG DIKAVELCLK SGAKISTQQH DLSTPVHLAC AQGAIDIVKL MFE MQPMEK RLCLSCTDVQ KMTPLHCASM FDHPDIVSYL VAEGADINAL DKEHRSPLLL AASRSGWKTV HLLIRLGACI SVKD AAARN VLHFVIMNGG RLTDFAEQVA NCQTQAQLKL LLNEKDSMGC SPLHYASRDG HIRSLENLIR LGACINLKNN NNESP LHFA ARYGRYNTVR QLLDSEKGSF IINESDGAGM TPLHISSQQG HTRVVQLLLN RGALLHRDHT GRNPLQLAAM SGYTET IEL LHSVHSHLLD QVDKDGNTAL HLATMENKPH AISVLMSMGC KLVYNVLDMS AIDYAIYYKY PEAALAMVTH EERANEV MA LRSDKHPCVT LALIASMPKV FEAVQDKCIT KANCKKDSKS FYIKYSFAFL QCPFMFAKID EKTGESITTA SPIPLPAL N TMVTHGRVEL LAHPLSQKYL QMKWNSYGKY FHLANLLIYS IFLVFVTIYS SLMMNNIELK AGDNKTMSQY CNMGWEQLT MNLSQNPSVA SQIRLDSCEE RINRTTAILF CAVVIVVYIL LNSMRELIQI YQQKLHYILE TVNLISWVLY ISALVMVTPA FQPDGGINT IHYSAASIAV FLSWFRLLLF LQRFDQVGIY VVMFLEILQT LIKVLMVFSI LIIAFGLAFY ILLSKIIDPQ P NHLSFSNI PMSLLRTFSM MLGELDFVGT YVNTYYRDQL KVPMTSFLIL SVFMILMPIL LMNLLIGLAV GDIESVRRNA QL KRLAMQV VLHTELERKL PHVWLQRVDK MELIEYPNET KCKLGFCDFI LRKWFSNPFT EDSSMDVISF DNNDDYINAE LER QRRKLR DISRMLEQQH HLVRLIVQKM EIKTEADDVD EGISPNELRS VVGLRSAGGN RWNSPRVRNK LRAALSFNKS M

UniProtKB: Transient receptor potential cation channel subfamily A member 1

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74515
FSC plot (resolution estimation)

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