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- PDB-6b5v: Structure of TRPV5 in complex with econazole -

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Database: PDB / ID: 6b5v
TitleStructure of TRPV5 in complex with econazole
DescriptorTransient receptor potential cation channel subfamily V member 5
KeywordsMEMBRANE PROTEIN / TRPV5 / Econazole / Transient Receptor Potential Channel / Cryo-EM
Specimen sourceOryctolagus cuniculus / mammal / Rabbit / アナウサギ /
MethodElectron microscopy (4.8 Å resolution / Particle / Single particle)
AuthorsHughes, T.E.T. / Lodowski, D.T. / Huynh, K.W. / Yazici, A. / del Rosario, J. / Kapoor, A. / Basak, S. / Samanta, A. / Chakrapani, S. / Zhou, Z.H. / Filizola, M. / Rohacs, T. / Han, S. / Moiseenkova-Bell, V.Y.
CitationNat. Struct. Mol. Biol., 2018, 25, 53-60

Nat. Struct. Mol. Biol., 2018, 25, 53-60 Yorodumi Papers
Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM.
Taylor E T Hughes / David T Lodowski / Kevin W Huynh / Aysenur Yazici / John Del Rosario / Abhijeet Kapoor / Sandip Basak / Amrita Samanta / Xu Han / Sudha Chakrapani / Z Hong Zhou / Marta Filizola / Tibor Rohacs / Seungil Han / Vera Y Moiseenkova-Bell

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Deposited unit
A: Transient receptor potential cation channel subfamily V member 5
B: Transient receptor potential cation channel subfamily V member 5
D: Transient receptor potential cation channel subfamily V member 5
C: Transient receptor potential cation channel subfamily V member 5
hetero molecules

Theoretical massNumber of molelcules
Total (without water)333,1659

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21520
ΔGint (kcal/M)-217
Surface area (Å2)131990


#1: Polypeptide(L)
Transient receptor potential cation channel subfamily V member 5 / TrpV5 / Epithelial calcium channel 1 / ECaC1 / Osm-9-like TRP channel 3 / OTRPC3

Mass: 82899.656 Da / Num. of mol.: 4
Source: (gene. exp.) Oryctolagus cuniculus / mammal / アナウサギ /
References: UniProt: Q9XSM3
#2: Chemical
ChemComp-ECL / 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole / R-Econazole

Mass: 381.684 Da / Num. of mol.: 4 / Formula: C18H15Cl3N2O
#3: ChemicalChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Full-length TRPV5 in complex with econazole / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Oryctolagus cuniculus
Source (recombinant)Organism: Saccharomyces cerevisiae / Strain: BJ5457
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
1150mMSodium ChlorideNaCl1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45455 / Cs: 2.7 mm
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3313
Image scansMovie frames/image: 50


SoftwareName: PHENIX / Version: dev_2870: / Classification: refinement
EM software
IDNameVersionCategoryImaging IDImage processing IDFitting ID
7Coot0.8.8-preMODEL FITTING1
Particle selectionNumber of particles selected: 925927
SymmetryPoint symmetry: C4
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 50566 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: correlation coefficient
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319612
ELECTRON MICROSCOPYf_angle_d0.81226652
ELECTRON MICROSCOPYf_dihedral_angle_d12.83811560
ELECTRON MICROSCOPYf_chiral_restr0.0422992
ELECTRON MICROSCOPYf_plane_restr0.0043324

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