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- PDB-6bgi: Cryo-EM structure of the TMEM16A calcium-activated chloride chann... -

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Database: PDB / ID: 6bgi
TitleCryo-EM structure of the TMEM16A calcium-activated chloride channel in nanodisc
ComponentsAnoctamin-1Calcium-dependent chloride channel
KeywordsMEMBRANE PROTEIN / chloride channel / TMEM16 family
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 / chloride transport / detection of temperature stimulus involved in sensory perception of pain / chloride channel activity / cation transport / chloride channel complex / chloride transmembrane transport / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of membrane potential / 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
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsDang, S. / Feng, S. / Tien, J. / Peters, C.J. / Bulkley, D. / Lolicato, M. / Zhao, J. / Zuberbuhler, K. / Ye, W. / Qi, J. / Chen, T. / Craik, C.S. / Jan, Y.N. / Minor Jr., D.L. / Cheng, Y. / Jan, L.Y.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 28, 2017 / Release: Dec 27, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 27, 2017Structure modelrepositoryInitial release
1.1Jan 10, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Deposited unit
A: Anoctamin-1
B: Anoctamin-1
hetero molecules

Theoretical massNumber of molelcules
Total (without water)211,3686

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1590
ΔGint (kcal/M)-72
Surface area (Å2)56780


#1: Protein/peptide Anoctamin-1 / Calcium-dependent chloride channel / Transmembrane protein 16A

Mass: 105603.984 Da / Num. of mol.: 2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ano1, Tmem16a / Production host: Homo sapiens (human) / References: UniProt: Q8BHY3
#2: Chemical

Mass: 40.078 Da / Num. of mol.: 4 / Formula: Ca / Calcium

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: TMEM16A in Nanodsic / Type: CELL / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 9
Buffer component
IDConc.NameFormulaBuffer ID
110 mMTris NitrateTrisNO31
2150 mMPotassium NitrateKNO31
31 mMCalcium ChlorideCaCl21
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot 6-8 seconds before plunging

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 / Calibrated magnification: 29000 / Calibrated defocus min: 900 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 80 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3149
Image scansMovie frames/image: 40 / Used frames/image: 1-40


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
1Gautomatch0.56particle selection
2SerialEM3.7betaimage acquisition
4Gctf0.1.06CTF correction
7UCSF Chimera1.11.2model fitting
9RELION2.1beta1initial Euler assignment
10RELION2.1beta1final Euler assignment
12RELION2.1beta13D reconstruction
13PHENIX1.10.1model refinement
14REFMAC5model refinement
CTF correctionType: NONE
Particle selectionNumber of particles selected: 927414
SymmetryPoint symmetry: C2
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 251851 / Algorithm: BACK PROJECTION / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0108786
ELECTRON MICROSCOPYf_angle_d0.97312285
ELECTRON MICROSCOPYf_dihedral_angle_d5.2494980
ELECTRON MICROSCOPYf_chiral_restr0.0501295
ELECTRON MICROSCOPYf_plane_restr0.0071409

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