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- PDB-6whg: PI3P and calcium bound full-length TRPY1 in detergent -

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Basic information

Entry
Database: PDB / ID: 6whg
TitlePI3P and calcium bound full-length TRPY1 in detergent
ComponentsCalcium channel YVC1
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


TRP channels / vacuole-mitochondrion membrane contact site / intracellular monoatomic cation homeostasis / voltage-gated monoatomic ion channel activity / fungal-type vacuole / calcium-activated cation channel activity / sodium channel activity / fungal-type vacuole membrane / calcium ion transmembrane import into cytosol / potassium channel activity ...TRP channels / vacuole-mitochondrion membrane contact site / intracellular monoatomic cation homeostasis / voltage-gated monoatomic ion channel activity / fungal-type vacuole / calcium-activated cation channel activity / sodium channel activity / fungal-type vacuole membrane / calcium ion transmembrane import into cytosol / potassium channel activity / plasma membrane => GO:0005886 / calcium ion import across plasma membrane / calcium channel activity / monoatomic ion channel activity
Similarity search - Function
Transient receptor potential cation channel subfamily V
Similarity search - Domain/homology
Chem-PWE / Calcium channel YVC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAhmed, T. / Moiseenkova-Bell, V.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103899 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129357 United States
CitationJournal: Structure / Year: 2022
Title: Structure of the ancient TRPY1 channel from Saccharomyces cerevisiae reveals mechanisms of modulation by lipids and calcium.
Authors: Tofayel Ahmed / Collin R Nisler / Edwin C Fluck / Sanket Walujkar / Marcos Sotomayor / Vera Y Moiseenkova-Bell /
Abstract: Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, ...Transient receptor potential (TRP) channels emerged in fungi as mechanosensitive osmoregulators. The Saccharomyces cerevisiae vacuolar TRP yeast 1 (TRPY1) is the most studied TRP channel from fungi, but the structure and details of channel modulation remain elusive. Here, we describe the full-length cryoelectron microscopy structure of TRPY1 at 3.1 Å resolution in a closed state. The structure, despite containing an evolutionarily conserved and archetypical transmembrane domain, reveals distinctive structural folds for the cytosolic N and C termini, compared with other eukaryotic TRP channels. We identify an inhibitory phosphatidylinositol 3-phosphate (PI(3)P) lipid-binding site, along with two Ca-binding sites: a cytosolic site, implicated in channel activation and a vacuolar lumen site, implicated in inhibition. These findings, together with data from microsecond-long molecular dynamics simulations and a model of a TRPY1 open state, provide insights into the basis of TRPY1 channel modulation by lipids and Ca, and the molecular evolution of TRP channels.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Calcium channel YVC1
B: Calcium channel YVC1
C: Calcium channel YVC1
D: Calcium channel YVC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,35016
Polymers312,1384
Non-polymers3,21112
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, TRP channels are known to form tetrameric assemblies
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Calcium channel YVC1 / TRP homolog / Yeast vacuolar conductance protein 1


Mass: 78034.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YVC1, YOR087W, YOR088W, YOR3151W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12324
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PWE / (2R)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2S,3S,4S,5S,6R)-2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propan-2-yl hexadecanoate


Mass: 722.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H56O16P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: PI3P and calcium bound full-length TRPY1 in detergent / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
10RELION3.1-beta-commit-b86482initial Euler assignment
11RELION3.1-beta-commit-b86482final Euler assignment
13RELION3.1-beta-commit-b864823D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55593 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00917468
ELECTRON MICROSCOPYf_angle_d1.128423644
ELECTRON MICROSCOPYf_chiral_restr0.06792680
ELECTRON MICROSCOPYf_plane_restr0.00892928
ELECTRON MICROSCOPYf_dihedral_angle_d25.16672380

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