[English] 日本語
- PDB-6bgj: Cryo-EM structure of the TMEM16A calcium-activated chloride chann... -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6bgj
TitleCryo-EM structure of the TMEM16A calcium-activated chloride channel in LMNG
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, L. / Chen, T. / Craik, C.S. / Jan, Y.N. / Minor, D.L.Jr. / 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

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


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

Theoretical massNumber of molelcules
Total (without water)211,2884

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1410
ΔGint (kcal/M)-33
Surface area (Å2)47930


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

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

Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: TMEM16A Calcium-activated chloride channel / 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
40.02mMLauryl Maltose Neopentyl GlycolLMNG1
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 FIELD / Calibrated magnification: 29000 / Calibrated defocus min: 800 nm / Calibrated defocus max: 1900 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
Details: 5326 images for TMEM16A alone in LMNG, 2556 images for TMEM16A with Fab bound in LMNG
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 2 / Number of real images: 7882
Image scansMovie frames/image: 40 / Used frames/image: 1-40


SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging ID
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_d0.0087609
ELECTRON MICROSCOPYf_angle_d1.18410370
ELECTRON MICROSCOPYf_dihedral_angle_d6.3124424
ELECTRON MICROSCOPYf_chiral_restr0.0611207
ELECTRON MICROSCOPYf_plane_restr0.0101301

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more