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Yorodumi- EMDB-9117: Structure of the human TRPV3 channel in a putative sensitized con... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9117 | ||||||||||||
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Title | Structure of the human TRPV3 channel in a putative sensitized conformation | ||||||||||||
Map data | Single-particle cryo-EM reconstruction of human TRPV3 in a putative sensitized state | ||||||||||||
Sample |
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Keywords | membrane protein / ion channel / TRP channel / calcium transport / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of hair cycle / TRP channels / response to temperature stimulus / positive regulation of calcium ion import / calcium ion transmembrane transport / calcium channel activity / receptor complex / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Zubcevic L / Herzik MA | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Conformational ensemble of the human TRPV3 ion channel. Authors: Lejla Zubcevic / Mark A Herzik / Mengyu Wu / William F Borschel / Marscha Hirschi / Albert S Song / Gabriel C Lander / Seok-Yong Lee / Abstract: Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin ...Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin physiology through the release of pro-inflammatory messengers. Mutations in trpv3 have been identified as the cause of the congenital skin disorder, Olmsted syndrome. Unlike other members of the thermoTRPV channel family, TRPV3 sensitizes upon repeated stimulation, yet a lack of structural information about the channel precludes a molecular-level understanding of TRPV3 sensitization and gating. Here, we present the cryo-electron microscopy structures of apo and sensitized human TRPV3, as well as several structures of TRPV3 in the presence of the common thermoTRPV agonist 2-aminoethoxydiphenyl borate (2-APB). Our results show α-to-π-helix transitions in the S6 during sensitization, and suggest a critical role for the S4-S5 linker π-helix during ligand-dependent gating. | ||||||||||||
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_9117.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-9117-v30.xml emd-9117.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_9117.png | 191.7 KB | ||
Filedesc metadata | emd-9117.cif.gz | 6.8 KB | ||
Others | emd_9117_half_map_1.map.gz emd_9117_half_map_2.map.gz | 269 MB 267.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9117 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9117 | HTTPS FTP |
-Related structure data
Related structure data | 6mhsMC 9115C 9119C 9120C 9121C 6mhoC 6mhvC 6mhwC 6mhxC C: citing same article (ref.) M: atomic model generated by this map |
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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_9117.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Single-particle cryo-EM reconstruction of human TRPV3 in a putative sensitized state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.91 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Even half map
File | emd_9117_half_map_1.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd half map
File | emd_9117_half_map_2.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human TRPV3 in a putative sensitized state
Entire | Name: Human TRPV3 in a putative sensitized state |
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Components |
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-Supramolecule #1: Human TRPV3 in a putative sensitized state
Supramolecule | Name: Human TRPV3 in a putative sensitized state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 94.860219 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEKAHPKEMV PLMGKRVAAP SGNPAILPEK RPAEITPTKK SAHFFLEIEG FEPNPTVAKT SPPVFSKPMD SNIRQCISGN CDDMDSPQS PQDDVTETPS NPNSPSAQLA KEEQRRKKRR LKKRIFAAVS EGCVEELVEL LVELQELCRR RHDEDVPDFL M HKLTASDT ...String: MEKAHPKEMV PLMGKRVAAP SGNPAILPEK RPAEITPTKK SAHFFLEIEG FEPNPTVAKT SPPVFSKPMD SNIRQCISGN CDDMDSPQS PQDDVTETPS NPNSPSAQLA KEEQRRKKRR LKKRIFAAVS EGCVEELVEL LVELQELCRR RHDEDVPDFL M HKLTASDT GKTCLMKALL NINPNTKEIV RILLAFAEEN DILGRFINAE YTEEAYEGQT ALNIAIERRQ GDIAALLIAA GA DVNAHAK GAFFNPKYQH EGFYFGETPL ALAACTNQPE IVQLLMEHEQ TDITSRDSRG NNILHALVTV AEDFKTQNDF VKR MYDMIL LRSGNWELET TRNNDGLTPL QLAAKMGKAE ILKYILSREI KEKRLRSLSR KFTDWAYGPV SSSLYDLTNV DTTT DNSVL EITVYNTNID NRHEMLTLEP LHTLLHMKWK KFAKHMFFLS FCFYFFYNIT LTLVSYYRPR EEEAIPHPLA LTHKM GWLQ LLGRMFVLIW AMCISVKEGI AIFLLRPSDL QSILSDAWFH FVFFIQAVLV ILSVFLYLFA YKEYLACLVL AMALGW ANM LYYTRGFQSM GMYSVMIQKV ILHDVLKFLF VYIVFLLGFG VALASLIEKC PKDNKDCSSY GSFSDAVLEL FKLTIGL GD LNIQQNSKYP ILFLFLLITY VILTFVLLLN MLIALMGETV ENVSKESERI WRLQRARTIL EFEKMLPEWL RSRFRMGE L CKVAEDDFRL CLRINEVKWT EWKTHVSFLN EDPGPVRRTD FNKIQDSSRN NSKTTLNAFE EVEEFPETSV VDAGLEVLF QGPAAAVDYK DDDDKAHHHH HHHHHH UniProtKB: Transient receptor potential cation channel subfamily V member 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.35 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER Details: Sample was manually blotted for 4 seconds prior to plunge-freezing into liquid ethane cooled by liquid nitrogen.. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 93.0 K / Max: 93.0 K |
Details | Alignment performed as described in Herzik, Wu, Lander, Nat Methods 2017 (PMID: 28991891) |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-47 / Number grids imaged: 1 / Number real images: 2982 / Average exposure time: 12.0 sec. / Average electron dose: 67.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 559206 |
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Startup model | Type of model: EMDB MAP EMDB ID: Details: Initial particles were 3D auto-refined using a 30-Angstrom low-pass-filtered apo TRPV3 structure (EMDB-9115) as the initial model. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 44554 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 51 / Target criteria: Correlation coefficient |
Output model | PDB-6mhs: |