[English] 日本語
Yorodumi- EMDB-23853: Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 4 degrees Celsius -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23853 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 4 degrees Celsius | |||||||||||||||
Map data | TRPV3 in MSP2N2 nanodiscs, closed state at 4 degrees Celsius | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation channel activity / monoatomic ion channel activity / calcium channel activity / lysosome / receptor complex / membrane ...negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation channel activity / monoatomic ion channel activity / calcium channel activity / lysosome / receptor complex / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.98 Å | |||||||||||||||
Authors | Neuberger A / Nadezhdin KD / Sobolevsky AI | |||||||||||||||
Funding support | United States, 4 items
| |||||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel. Authors: Kirill D Nadezhdin / Arthur Neuberger / Yuri A Trofimov / Nikolay A Krylov / Viktor Sinica / Nikita Kupko / Viktorie Vlachova / Eleonora Zakharian / Roman G Efremov / Alexander I Sobolevsky / Abstract: Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been ...Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23853.map.gz | 12.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23853-v30.xml emd-23853.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_23853.png | 150.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23853 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23853 | HTTPS FTP |
-Validation report
Summary document | emd_23853_validation.pdf.gz | 369.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23853_full_validation.pdf.gz | 369.2 KB | Display | |
Data in XML | emd_23853_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_23853_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23853 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23853 | HTTPS FTP |
-Related structure data
Related structure data | 7mijMC 7mikC 7milC 7mimC 7minC 7mioC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23853.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | TRPV3 in MSP2N2 nanodiscs, closed state at 4 degrees Celsius | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Transient receptor potential cation channel subfamily V member 3
Entire | Name: Transient receptor potential cation channel subfamily V member 3 |
---|---|
Components |
|
-Supramolecule #1: Transient receptor potential cation channel subfamily V member 3
Supramolecule | Name: Transient receptor potential cation channel subfamily V member 3 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 924.7 KDa |
-Macromolecule #1: Transient receptor potential cation channel subfamily V member 3
Macromolecule | Name: Transient receptor potential cation channel subfamily V member 3 type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 92.630695 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNAHSKEMAP LMGKRTTAPG GNPVVLTEKR PADLTPTKKS AHFFLEIEGF EPNPTVTKTS PPIFSKPMDS NIRQCLSGNC DDMDSPQSP QDDVTETPSN PNSPSANLAK EEQRQKKKRL KKRIFAAVSE GCVEELRELL QDLQDLCRRR RGLDVPDFLM H KLTASDTG ...String: MNAHSKEMAP LMGKRTTAPG GNPVVLTEKR PADLTPTKKS AHFFLEIEGF EPNPTVTKTS PPIFSKPMDS NIRQCLSGNC DDMDSPQSP QDDVTETPSN PNSPSANLAK EEQRQKKKRL KKRIFAAVSE GCVEELRELL QDLQDLCRRR RGLDVPDFLM H KLTASDTG KTCLMKALLN INPNTKEIVR ILLAFAEEND ILDRFINAEY TEEAYEGQTA LNIAIERRQG DITAVLIAAG AD VNAHAKG VFFNPKYQHE GFYFGETPLA LAACTNQPEI VQLLMENEQT DITSQDSRGN NILHALVTVA EDFKTQNDFV KRM YDMILL RSGNWELETM RNNDGLTPLQ LAAKMGKAEI LKYILSREIK EKPLRSLSRK FTDWAYGPVS SSLYDLTNVD TTTD NSVLE IIVYNTNIDN RHEMLTLEPL HTLLHTKWKK FAKYMFFLSF CFYFFYNITL TLVSYYRPRE DEDLPHPLAL THKMS WLQL LGRMFVLIWA TCISVKEGIA IFLLRPSDLQ SILSDAWFHF VFFVQAVLVI LSVFLYLFAY KEYLACLVLA MALGWA NML YYTRGFQSMG MYSVMIQKVI LHDVLKFLFV YILFLLGFGV ALASLIEKCS KDKKDCSSYG SFSDAVLELF KLTIGLG DL NIQQNSTYPI LFLFLLITYV ILTFVLLLNM LIALMGETVE NVSKESERIW RLQRARTILE FEKMLPEWLR SRFRMGEL C KVADEDFRLC LRINEVKWTE WKTHVSFLNE DPGPIRRTAD LNKIQDSSRS NSKTTLYAFD ELDEFPETSV LVPRGSAAA WSHPQFEK |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 36 / Formula: POV |
---|---|
Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2 |
---|---|
Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 328 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.6 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||||||||
Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9702 / Average exposure time: 2.5 sec. / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-7mij: |