+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23491 | |||||||||||||||
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Title | Structure of squirrel TRPV1 in apo state | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Transient Receptor Potential V Family Member 1 / TRP channel / TRPV1 full length / TRPV1 wild type / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane ...temperature-gated ion channel activity / response to capsazepine / sensory perception of mechanical stimulus / peptide secretion / detection of chemical stimulus involved in sensory perception of pain / smooth muscle contraction involved in micturition / cellular response to acidic pH / fever generation / detection of temperature stimulus involved in thermoception / dendritic spine membrane / behavioral response to pain / diet induced thermogenesis / calcium ion import across plasma membrane / detection of temperature stimulus involved in sensory perception of pain / extracellular ligand-gated monoatomic ion channel activity / phosphoprotein binding / calcium channel activity / lipid metabolic process / cellular response to heat / postsynaptic membrane / calmodulin binding / negative regulation of transcription by RNA polymerase II / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Ictidomys tridecemlineatus (thirteen-lined ground squirrel) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||||||||
Authors | Nadezhdin KD / Neuberger A | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Extracellular cap domain is an essential component of the TRPV1 gating mechanism. Authors: Kirill D Nadezhdin / Arthur Neuberger / Yury A Nikolaev / Lyle A Murphy / Elena O Gracheva / Sviatoslav N Bagriantsev / Alexander I Sobolevsky / Abstract: Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the ...Transient receptor potential (TRP) channels are polymodal molecular sensors involved in numerous physiological processes and implicated in a variety of human diseases. Several structures of the founding member of the TRP channel family, TRPV1, are available, all of which were determined for the protein missing the N- and C-termini and the extracellular S5-P-loop. Here, we present structures of the full-length thirteen-lined ground squirrel TRPV1 solved by cryo-EM. Our structures resolve the extracellular cap domain formed by the S5-P-loops and the C-terminus that wraps around the three-stranded β-sheet connecting elements of the TRPV1 intracellular skirt. The cap domain forms a dome above the pore's extracellular entrance, with four portals leading to the ion conductance pathway. Deletion of the cap increases the TRPV1 average conductance, reduces the open probability and affects ion selectivity. Our data show that both the termini and the cap domain are critical determinants of TRPV1 function. | |||||||||||||||
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_23491.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-23491-v30.xml emd-23491.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_23491.png | 167.4 KB | ||
Filedesc metadata | emd-23491.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23491 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23491 | HTTPS FTP |
-Validation report
Summary document | emd_23491_validation.pdf.gz | 405 KB | Display | EMDB validaton report |
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Full document | emd_23491_full_validation.pdf.gz | 404.6 KB | Display | |
Data in XML | emd_23491_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_23491_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23491 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23491 | HTTPS FTP |
-Related structure data
Related structure data | 7lqyMC 7lqzC 7lr0C 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_23491.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
-Entire : sample 1
Entire | Name: sample 1 |
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Components |
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-Supramolecule #1: sample 1
Supramolecule | Name: sample 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Ictidomys tridecemlineatus (thirteen-lined ground squirrel) |
-Macromolecule #1: Osm-9-like TRP channel 1
Macromolecule | Name: Osm-9-like TRP channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Ictidomys tridecemlineatus (thirteen-lined ground squirrel) |
Molecular weight | Theoretical: 95.902781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKKWANLDSG ESEDPPHEDS CPDPPDGDPN SKQSPAKPHI FSTTKSRTRL FGKGDSEEAS PMDCSYEEGE LASCPTITVS SVVIIQRPG DALTCARQLS QDSVSAGAEK PLKLYDRRSI FDAVAQNNCQ ELESLLPFLQ KSRKRLTDSE FKDPETGKTC L LKAMLNLH ...String: MKKWANLDSG ESEDPPHEDS CPDPPDGDPN SKQSPAKPHI FSTTKSRTRL FGKGDSEEAS PMDCSYEEGE LASCPTITVS SVVIIQRPG DALTCARQLS QDSVSAGAEK PLKLYDRRSI FDAVAQNNCQ ELESLLPFLQ KSRKRLTDSE FKDPETGKTC L LKAMLNLH NGQNDTISLL LDIARQTDSL KEFVNASYTD SYYKGQTALH IAIERRNMAL VTLLVENGAD VQAAANGDFF KK TKGRPGF YFGELPLSLA ACTNQLAIVK FLLQNSWQPA DISARDSVGN TVLHALVEVA DNTADNTKFV TSMYNEILIL GAK LHPTLK LEELINKKGL TPLALAASSG KIGVLAYILQ REIQEPECRH LSRKFTEWAY GPVHSSLYDL SCIDTCEKNS VLEV IAYSS SETPNRHDML LVEPLNRLLQ DKWDRFVKRI FYFNFFVYCL YMIVFTTAAY YRPVDGLPPY KLKNTVGDYF RVTGE ILSV SGGVYFFLRG IQYFLQRRPS MKTLFVDSYS EMLFFVQSLF MLGSVVLYFS HRKEYVASMV FSLAMGWTNM LYYTRG FQQ MGIYAVMIEK MILRDLCRFM FVYLVFLFGF STAVVTLIED GKNYSEPAEY TSHRWRAPGC RPPDSYNSLY STCLELF KF TIGMGDLEFT ENYDFKAVFI ILLLAYVILT YILLLNMLIA LMGETVNKIA QESKNIWKLQ RAITILDTEK SFLKCMRK A FRSGKLLQVG YTPDGKDDYR WCFRVDEVNW TTWNTNVGII NEDPGNCEGV KRTLSFSLRS GRVSGRNWRN FALVPLLRD ASTRDRHHAQ PEEVHLKHFA GSLKPEDAEV FKDSMAPGEK LPVR UniProtKB: Transient receptor potential cation channel subfamily V member 1 |
-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: 32 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol / type: ligand / ID: 3 / Number of copies: 4 / Formula: YBG |
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Molecular weight | Theoretical: 837.069 Da |
Chemical component information | ChemComp-YBG: |
-Macromolecule #4: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #5: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 5 / Number of copies: 1 |
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Molecular weight | Theoretical: 22.99 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.8 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Slit width: 30 eV |
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: 11191 / Average exposure time: 2.5 sec. / Average electron dose: 65.0 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: -2.5 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 |
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Output model | PDB-7lqy: |