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- EMDB-4748: CryoEM structure of calcium-free human TMEM16K / Anoctamin 10 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4748
TitleCryoEM structure of calcium-free human TMEM16K / Anoctamin 10 in detergent (closed form)
Map data
SampleAnoctamin 10Calcium-dependent chloride channel
  • Anoctamin-10Calcium-dependent chloride channel
Function / homology
Function and homology information


Stimuli-sensing channels / intracellular calcium activated chloride channel activity / calcium activated cation channel activity / chloride transport / cation transport / ion transmembrane transport / membrane / integral component of membrane / plasma membrane
Anoctamin / Anoctamin-10 / Calcium-activated chloride channel
Anoctamin-10
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.14 Å
AuthorsPike ACW / Bushell SR / Shintre CA / Tessitore A / Chu A / Mukhopadhyay S / Shrestha L / Chalk R / Burgess-Brown NA / Love J / Huiskonen JT / Edwards AM / Arrowsmith CH / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: CryoEM structure of calcium-free human TMEM16K / Anoctamin 10 in detergent (closed form)
Authors: Pike ACW / Bushell SR / Shintre CA / Tessitore A / Chu A / Mukhopadhyay S / Shrestha L / Chalk R / Burgess-Brown NA / Love J / Huiskonen JT / Edwards AM / Arrowsmith CH / Bountra C / Carpenter EP / Structural Genomics Consortium (SGC)
Validation ReportPDB-ID: 6r7z

SummaryFull reportAbout validation report
DateDeposition: Mar 29, 2019 / Header (metadata) release: May 1, 2019 / Map release: May 1, 2019 / Update: May 15, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6r7z
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4748.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 200 pix.
= 164.4 Å
0.82 Å/pix.
x 200 pix.
= 164.4 Å
0.82 Å/pix.
x 200 pix.
= 164.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.01239343 - 0.038761023
Average (Standard dev.)0.0017136736 (±0.003567372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 164.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z164.400164.400164.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0120.0390.002

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Supplemental data

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Mask #1

Fileemd_4748_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Anoctamin 10

EntireName: Anoctamin 10Calcium-dependent chloride channel / Number of components: 2

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Component #1: cellular-component, Anoctamin 10

Cellular-componentName: Anoctamin 10Calcium-dependent chloride channel / Recombinant expression: No
MassTheoretical: 153 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: PFB-CT10HF-LIC

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Component #2: protein, Anoctamin-10

ProteinName: Anoctamin-10Calcium-dependent chloride channel / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 77.276016 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 % / Details: blot for 4.5sec before plunging.

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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: 56.5 e/Å2 / Illumination mode: SPOT SCAN
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2750.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2038

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 23607
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 5.14 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation coef / Refinement space: REAL
Details: phenix.real_space_refine with NCS constraints and model reference restraints (PDB id: TBC).
Overall bvalue: 150
Output model

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