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- EMDB-7058: Structure of TRPV5 in complex with econazole -

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Basic information

Entry
Database: EMDB / ID: 7058
TitleStructure of TRPV5 in complex with econazole
Map dataTRPV5 in complex with econazole
SampleFull-length TRPV5 in complex with econazole
  • Transient receptor potential cation channel subfamily V member 5
  • (ligand) x 2
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 / Transient receptor potential channel / 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
SourceOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsHughes TET / Lodowski DT
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 ReportPDB-ID: 6b5v

SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Dec 27, 2017 / Last update: Jan 31, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6b5v
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7058.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.1 Å/pix.
= 211.2 Å
192 pix
1.1 Å/pix.
= 211.2 Å
192 pix
1.1 Å/pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.07627523 - 0.13983618
Average (Standard dev.)0.0016641174 (0.008344924)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-192-1920
Limit-1-1191
Spacing192192192
CellA=B=C: 211.20001 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-1920
NC/NR/NS192192192
D min/max/mean-0.0760.1400.002

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Supplemental data

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Sample components

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Entire Full-length TRPV5 in complex with econazole

EntireName: Full-length TRPV5 in complex with econazole / Number of components: 4

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Component #1: protein, Full-length TRPV5 in complex with econazole

ProteinName: Full-length TRPV5 in complex with econazole / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5457

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Component #2: protein, Transient receptor potential cation channel subfamily V ...

ProteinName: Transient receptor potential cation channel subfamily V member 5
Recombinant expression: No
MassTheoretical: 82.899656 kDa
Source (engineered)Expression System: Oryctolagus cuniculus (rabbit)

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Component #3: ligand, 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)eth...

LigandName: 1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.381684 kDa

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Component #4: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2.5 mg/ml / pH: 8
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 45455 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3313

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50566
3D reconstructionSoftware: RELION / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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