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

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Basic information

Entry
Database: PDB / ID: 6b5v
TitleStructure of TRPV5 in complex with econazole
ComponentsTransient receptor potential cation channel subfamily V member 5
KeywordsMEMBRANE PROTEIN / TRPV5 / Econazole / Transient Receptor Potential Channel / Cryo-EM
Function / homologyAnkyrin repeat / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V member 5 ...Ankyrin repeat / Transient receptor potential cation channel subfamily V member 5/6 / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ion transport protein / Ankyrin repeat-containing domain superfamily / Transient receptor potential cation channel subfamily V / Ankyrin repeat-containing domain / Transient receptor potential cation channel subfamily V member 5 / in:ipr004729: / Ion transport domain / calcium ion import across plasma membrane / calcium ion homeostasis / regulation of urine volume / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / protein tetramerization / protein homotetramerization / apical plasma membrane / calmodulin binding / integral component of plasma membrane / metal ion binding / Transient receptor potential cation channel subfamily V member 5
Function and homology information
Specimen sourceOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
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.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM.
Authors: 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
1.2Jan 31, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

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
Polyers331,5994
Non-polymers1,5675
Water0
1


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

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Components

#1: Protein/peptide
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 (rabbit) / Gene: Trpv5, Ecac1 / Production host: Saccharomyces cerevisiae (baker's yeast) / Strain (production host): BJ5457 / 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: Chemical ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full-length TRPV5 in complex with econazole / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5457
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
1150 mMSodium ChlorideNaCl1
220 mMHEPESC8H18N2O4S1
30.064 mMDMNGC43H80O221
42 mMTCEPC9H15O6P1
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

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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 FIELDBright-field microscopy / 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

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Processing

SoftwareName: PHENIX / Version: dev_2870: / Classification: refinement
EM software
IDNameVersionCategory
2Leginon0.1image acquisition
4Gctf1.06CTF correction
7Coot0.8.8-premodel fitting
9PHENIX1.12rc0model refinement
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
13RELION2.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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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