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

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Basic information

Entry
Database: PDB / ID: 6bgi
TitleCryo-EM structure of the TMEM16A calcium-activated chloride channel in nanodisc
DescriptorAnoctamin-1
KeywordsMEMBRANE PROTEIN / chloride channel / TMEM16 family
Specimen sourceMus musculus / mammal / Mouse / ハツカネズミ, はつかねずみ /
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
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.
CitationNature, 2017, 552, 426-429

Nature, 2017, 552, 426-429 Yorodumi Papers
Cryo-EM structures of the TMEM16A calcium-activated chloride channel.
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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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,3686
Polyers211,2082
Non-polymers1604
Water0
#1


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

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Components

#1: Polypeptide(L)Anoctamin-1 / Transmembrane protein 16A


Mass: 105603.984 Da / Num. of mol.: 2
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ /
References: UniProt: Q8BHY3
#2: Chemical
ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: TMEM16A in Nanodsic / Type: CELL / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus
Source (recombinant)Organism: Homo sapiens
Buffer solutionpH: 9
Buffer component
IDConc.UnitsNameFormulaBuffer ID
110mMTris NitrateTrisNO31
2150mMPotassium NitrateKNO31
31mMCalcium 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

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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 FIELD / Calibrated magnification: 29000 / Calibrated defocus min: 900 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm / 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

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1Gautomatch0.56PARTICLE SELECTION1
2SerialEM3.7betaIMAGE ACQUISITION1
4Gctf0.1.06CTF CORRECTION1
7UCSF Chimera1.11.2MODEL FITTING1
9RELION2.1beta1INITIAL EULER ASSIGNMENT1
10RELION2.1beta1FINAL EULER ASSIGNMENT1
11RELION2.1beta1CLASSIFICATION1
12RELION2.1beta1RECONSTRUCTION1
13PHENIX1.10.1MODEL REFINEMENT1
14REFMAC5MODEL REFINEMENT1
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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