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- EMDB-7096: Cryo-EM structure of the TMEM16A calcium-activated chloride chann... -

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Basic information

Entry
Database: EMDB / ID: 7096
TitleCryo-EM structure of the TMEM16A calcium-activated chloride channel in LMNG
Map datasharpened map
SampleTMEM16A Calcium-activated chloride channel
  • Anoctamin-1Calcium-dependent chloride channel
  • ligand
Function / homologyStimuli-sensing channels / Dimerisation domain of Ca+-activated chloride-channel, anoctamin / Calcium-activated chloride channel / Anoctamin, dimerisation domain / Anoctamin-1 / Anoctamin / iodide transmembrane transporter activity / intracellular calcium activated chloride channel activity / iodide transport / trachea development ...Stimuli-sensing channels / Dimerisation domain of Ca+-activated chloride-channel, anoctamin / Calcium-activated chloride channel / Anoctamin, dimerisation domain / Anoctamin-1 / Anoctamin / iodide transmembrane transporter activity / intracellular calcium activated chloride channel activity / iodide transport / trachea development / calcium activated cation channel activity / voltage-gated chloride channel activity / cation transport / chloride transport / chloride channel activity / detection of temperature stimulus involved in sensory perception of pain / chloride channel complex / chloride transmembrane transport / regulation of membrane potential / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to heat / apical plasma membrane / external side of plasma membrane / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytoplasm / Anoctamin-1
Function and homology information
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsDang S / Feng S
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structures of the TMEM16A calcium-activated chloride channel.
Authors: Shangyu Dang / Shengjie Feng / Jason Tien / Christian J Peters / David Bulkley / Marco Lolicato / Jianhua Zhao / Kathrin Zuberbühler / Wenlei Ye / Lijun Qi / Tingxu Chen / Charles S Craik / Yuh Nung Jan / Daniel L Minor / Yifan Cheng / Lily Yeh Jan
Validation ReportPDB-ID: 6bgj

SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 27, 2017 / Last update: Apr 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6bgj
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7096.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.02 Å/pix.
= 261.12 Å
256 pix
1.02 Å/pix.
= 261.12 Å
256 pix
1.02 Å/pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour Level:5.5 (by author), 5.5 (movie #1):
Minimum - Maximum-25.658325000000001 - 36.385463999999999
Average (Standard dev.)-0.000000003603186 (1.)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 261.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z261.120261.120261.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-25.65836.385-0.000

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Supplemental data

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Sample components

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Entire TMEM16A Calcium-activated chloride channel

EntireName: TMEM16A Calcium-activated chloride channel / Number of components: 3

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Component #1: cellular-component, TMEM16A Calcium-activated chloride channel

Cellular-componentName: TMEM16A Calcium-activated chloride channel / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #2: protein, Anoctamin-1

ProteinName: Anoctamin-1Calcium-dependent chloride channel / Details: Calcium ionsCalcium / Recombinant expression: No
MassTheoretical: 105.603984 kDa
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #3: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 2 / 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.: 0.5 mg/ml / pH: 9
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 1 % / Details: blot 6-8 seconds 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: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 7882
Details: 5326 images for TMEM16A alone in LMNG, 2556 images for TMEM16A with Fab bound in LMNG
Raw dataEMPIAR-10124 (Title: Cryo-EM structure of the TMEM16A in LMNG / Data size: 244.2
Data #1: Particle stacks extracted from motion corrected micrographs of TMEM16A in LMNG [picked particles - single frame - processed]
Data #2: Particle stacks extracted from motion corrected micrographs of TMEM16A bound with Fab in LMNG [picked particles - single frame - processed])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 251851
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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