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- PDB-7ykr: Structure of TRPA1 in Drosophila melanogaster in a state with 17 ... -

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Basic information

Entry
Database: PDB / ID: 7ykr
TitleStructure of TRPA1 in Drosophila melanogaster in a state with 17 ankyrin repeats determined
ComponentsTransient receptor potential cation channel subfamily A member 1
KeywordsMEMBRANE PROTEIN / ion channel / TRPA1
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 / phototransduction / monoatomic cation transport / ligand-gated monoatomic ion channel activity / response to light stimulus / monoatomic cation channel activity / positive regulation of calcium-mediated signaling / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun, L. / Liu, X. / Yang, Z. / Wang, X.
Funding support China, 4items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 2.0Oct 4, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_contact_author / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conf / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.pdbx_dist_value
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transient receptor potential cation channel subfamily A member 1
D: Transient receptor potential cation channel subfamily A member 1
B: Transient receptor potential cation channel subfamily A member 1
C: Transient receptor potential cation channel subfamily A member 1


Theoretical massNumber of molelcules
Total (without water)541,2974
Polymers541,2974
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Transient receptor potential cation channel subfamily A member 1 / dTRPA1 / Ankyrin-like with transmembrane domains protein 1 / dANKTM1


Mass: 135324.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: TrpA1, Anktm1, CG5751 / Plasmid: pEG BacMam / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q7Z020

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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: Homotetramer of dTRPA1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 2300 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74515 / Symmetry type: POINT

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