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- EMDB-21672: PI3P and calcium bound full-length TRPY1 in detergent -

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Basic information

Entry
Database: EMDB / ID: EMD-21672
TitlePI3P and calcium bound full-length TRPY1 in detergent
Map datafinal post-processed map
Sample
  • Complex: PI3P and calcium bound full-length TRPY1 in detergent
    • Protein or peptide: Calcium channel YVC1
  • Ligand: CALCIUM ION
  • Ligand: (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
KeywordsIon channel / MEMBRANE PROTEIN
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 / fungal-type vacuole membrane / calcium ion transmembrane import into cytosol / sodium channel activity / calcium ion import across plasma membrane ...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 / fungal-type vacuole membrane / calcium ion transmembrane import into cytosol / sodium channel activity / calcium ion import across plasma membrane / potassium channel activity / calcium channel activity / plasma membrane
Similarity search - Function
: / : / : / TRPY1 N-terminal linker helical domain / Calcium channel YVC1-like, C-terminal
Similarity search - Domain/homology
Calcium channel YVC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAhmed T / Moiseenkova-Bell VY
Funding support United States, 2 items
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, 2020-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0542
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0542
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6whg
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21672.png

Downloads & links

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Map

FileDownload / File: emd_21672.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal post-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0342 / Movie #1: 0.0542
Minimum - Maximum-0.12458728 - 0.23366089
Average (Standard dev.)-0.00010504299 (±0.0069180364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1250.234-0.000

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Supplemental data

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Mask #1

Fileemd_21672_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map2

Fileemd_21672_half_map_1.map
AnnotationHalf map2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map1

Fileemd_21672_half_map_2.map
AnnotationHalf map1
Projections & Slices
AxesZYX

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Sample components

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Entire : PI3P and calcium bound full-length TRPY1 in detergent

EntireName: PI3P and calcium bound full-length TRPY1 in detergent
Components
  • Complex: PI3P and calcium bound full-length TRPY1 in detergent
    • Protein or peptide: Calcium channel YVC1
  • Ligand: CALCIUM ION
  • Ligand: (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

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Supramolecule #1: PI3P and calcium bound full-length TRPY1 in detergent

SupramoleculeName: PI3P and calcium bound full-length TRPY1 in detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Calcium channel YVC1

MacromoleculeName: Calcium channel YVC1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 78.034602 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVSANGDLHL PISNEQCMPE NNGSLGFEAP TPRQILRVTL NLKYLIDKVV PIVYDPNDIV CDHSEILSPK VVKLAYEACG GNPKDKANK RKYQSVIIFS LLKVCEWYSI LATMEVHNAK LYETRNLASQ QLCKLLIERE ETRDLQFLFM QLLLRRYVIN E NDEDQEPL ...String:
MVSANGDLHL PISNEQCMPE NNGSLGFEAP TPRQILRVTL NLKYLIDKVV PIVYDPNDIV CDHSEILSPK VVKLAYEACG GNPKDKANK RKYQSVIIFS LLKVCEWYSI LATMEVHNAK LYETRNLASQ QLCKLLIERE ETRDLQFLFM QLLLRRYVIN E NDEDQEPL NALELATDMH CTTVIGSSGF QRCLKWIWRG WIVQNGLDPT TFIKDDSLAE VSLISHFNPV RLKAPVYQNY LQ MIFSFLF LGLYTLVVNG KDSERVQSFD LLESIFYVFN TGFILDELTK LYYIGYAHLS FWNLFNDTTY LIITFAMGFR AMS VTPLNA KYSSEDWDKI SYRVLSCAAP FVWSRLLLYL ESQRFIGIML VILKHMMKES IVFFFLLFLI MIGFTQGFLG LDSA DGKRD ITGPILGNLT ITVLGLGSFD VFEEFAPPYA AILYYGYYFI VSVILLNILI ALYSTAYQKV IDNADDEYMA LMSQK TLRY IRAPDEDVYV SPLNLIEVFM TPIFRILPPK RAKDLSYTVM TIVYSPFLLL ISVKETREAR RIKYNRMKRL NDDANE YDT PWDLTDGYLD DDDGLFSDNR NSGMRATQLK NSRSLKLQRT AEQEDVHFKV PKKWYKNVKK CSPSFEQYDN DDTEDDA GE DKDEVKELTK KVENLTAVIT DLLEKLDIKD KKE

UniProtKB: Calcium channel YVC1

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: (2R)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2S,3S,4S,5S,6R)-2,3,4,6...

MacromoleculeName: (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
type: ligand / ID: 3 / Number of copies: 4 / Formula: PWE
Molecular weightTheoretical: 722.693 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial model was generated from the data in hand using RELION. Only RELION is used to process data throughout.
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1-beta-commit-b86482) / Number images used: 55593
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta-commit-b86482) / Details: Only RELION is used to process data throughout.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1-beta-commit-b86482) / Details: Only RELION is used to process data throughout.
FSC plot (resolution estimation)

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