|Entry||Database: EMDB / ID: 7058|
|Title||Structure of TRPV5 in complex with econazole|
|Sample||Full-length TRPV5 in complex with econazole|
|Source||Oryctolagus cuniculus / mammal / アナウサギ /|
|Map data||TRPV5 in complex with econazole|
|Method||single particle reconstruction, at 4.8 Å resolution|
|Authors||Hughes TET / Lodowski DT|
|Citation||Nat. Struct. Mol. Biol., 2018, 25, 53-60|
Nat. Struct. Mol. Biol., 2018, 25, 53-60 Yorodumi Papers
|Validation Report||PDB-ID: 6b5v|
SummaryFull reportAbout validation report
|Date||Deposition: Sep 29, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Dec 27, 2017 / Last update: Jan 17, 2018|
Downloads & links
|File||emd_7058.map.gz (map file in CCP4 format, 28312 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire Full-length TRPV5 in complex with econazole
|Entire||Name: Full-length TRPV5 in complex with econazole / Number of components: 4|
-Component #1: protein, Full-length TRPV5 in complex with econazole
|Protein||Name: Full-length TRPV5 in complex with econazole / Recombinant expression: No|
|Source||Species: Oryctolagus cuniculus / mammal / アナウサギ /|
|Source (engineered)||Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ / |
-Component #2: protein, Transient receptor potential cation channel subfamily V ...
|Protein||Name: Transient receptor potential cation channel subfamily V member 5|
Recombinant expression: No
|Mass||Theoretical: 82.899656 kDa|
|Source (engineered)||Expression System: Oryctolagus cuniculus / mammal / アナウサギ /|
-Component #3: ligand, 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)eth...
Number of Copies: 4 / Recombinant expression: No
|Mass||Theoretical: 0.381684 kDa|
-Component #4: ligand, CALCIUM ION
|Ligand||Name: CALCIUM ION / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 4.007805 MDa|
|Sample solution||Specimen conc.: 2.5 mg/ml / pH: 8|
|Vitrification||Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 45455 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 3313|
|Processing||Method: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50566|
|3D reconstruction||Software: RELION / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution assessment)|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
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