+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21672 | |||||||||
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Title | PI3P and calcium bound full-length TRPY1 in detergent | |||||||||
Map data | final post-processed map | |||||||||
Sample |
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Keywords | Ion 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 / calcium-activated cation channel activity / fungal-type vacuole / sodium channel activity / calcium ion transmembrane import into cytosol / fungal-type vacuole membrane / calcium ion import across plasma membrane ...TRP channels / vacuole-mitochondrion membrane contact site / intracellular monoatomic cation homeostasis / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / fungal-type vacuole / sodium channel activity / calcium ion transmembrane import into cytosol / fungal-type vacuole membrane / calcium ion import across plasma membrane / plasma membrane => GO:0005886 / potassium channel activity / calcium channel activity / monoatomic ion channel activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Ahmed T / Moiseenkova-Bell VY | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21672.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-21672-v30.xml emd-21672.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21672_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_21672.png | 104 KB | ||
Masks | emd_21672_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-21672.cif.gz | 5.7 KB | ||
Others | emd_21672_half_map_1.map.gz emd_21672_half_map_2.map.gz | 45.7 MB 45.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21672 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21672 | HTTPS FTP |
-Validation report
Summary document | emd_21672_validation.pdf.gz | 997.2 KB | Display | EMDB validaton report |
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Full document | emd_21672_full_validation.pdf.gz | 996.7 KB | Display | |
Data in XML | emd_21672_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_21672_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21672 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21672 | HTTPS FTP |
-Related structure data
Related structure data | 6whgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21672.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | final post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21672_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map2
File | emd_21672_half_map_1.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1
File | emd_21672_half_map_2.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PI3P and calcium bound full-length TRPY1 in detergent
Entire | Name: PI3P and calcium bound full-length TRPY1 in detergent |
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Components |
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-Supramolecule #1: PI3P and calcium bound full-length TRPY1 in detergent
Supramolecule | Name: PI3P and calcium bound full-length TRPY1 in detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Calcium channel YVC1
Macromolecule | Name: Calcium channel YVC1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 78.034602 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #3: (2R)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2S,3S,4S,5S,6R)-2,3,4,6...
Macromolecule | Name: (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 |
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Molecular weight | Theoretical: 722.693 Da |
Chemical component information | ChemComp-PWE: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |