+Open data
-Basic information
Entry | Database: PDB / ID: 8d1n | ||||||||||||
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Title | bBest2_345 Ca2+-bound open state | ||||||||||||
Components | Bestrophin | ||||||||||||
Keywords | TRANSPORT PROTEIN / Ion channel / chloride channel / anion channel / pentamer | ||||||||||||
Function / homology | Function and homology information intracellularly ligand-gated monoatomic ion channel activity / ligand-gated monoatomic anion channel activity / Stimuli-sensing channels / bicarbonate channel activity / bicarbonate transport / chloride channel activity / ligand-gated monoatomic cation channel activity / chloride channel complex / basolateral plasma membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Bos taurus (cattle) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.93 Å | ||||||||||||
Authors | Owji, A.P. / Kittredge, A. / Hendrickson, W.A. / Tingting, Y. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structures and gating mechanisms of human bestrophin anion channels. Authors: Aaron P Owji / Jiali Wang / Alec Kittredge / Zada Clark / Yu Zhang / Wayne A Hendrickson / Tingting Yang / Abstract: Bestrophin-1 (Best1) and bestrophin-2 (Best2) are two members of the bestrophin family of calcium (Ca)-activated chloride (Cl) channels with critical involvement in ocular physiology and direct ...Bestrophin-1 (Best1) and bestrophin-2 (Best2) are two members of the bestrophin family of calcium (Ca)-activated chloride (Cl) channels with critical involvement in ocular physiology and direct pathological relevance. Here, we report cryo-EM structures of wild-type human Best1 and Best2 in various states at up to 1.8 Å resolution. Ca-bound Best1 structures illustrate partially open conformations at the two Ca-dependent gates of the channels, in contrast to the fully open conformations observed in Ca-bound Best2, which is in accord with the significantly smaller currents conducted by Best1 in electrophysiological recordings. Comparison of the closed and open states reveals a C-terminal auto-inhibitory segment (AS), which constricts the channel concentrically by wrapping around the channel periphery in an inter-protomer manner and must be released to allow channel opening. Our results demonstrate that removing the AS from Best1 and Best2 results in truncation mutants with similar activities, while swapping the AS between Best1 and Best2 results in chimeric mutants with swapped activities, underlying a key role of the AS in determining paralog specificity among bestrophins. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d1n.cif.gz | 388.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d1n.ent.gz | 330.7 KB | Display | PDB format |
PDBx/mmJSON format | 8d1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d1n_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8d1n_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8d1n_validation.xml.gz | 72.6 KB | Display | |
Data in CIF | 8d1n_validation.cif.gz | 91.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/8d1n ftp://data.pdbj.org/pub/pdb/validation_reports/d1/8d1n | HTTPS FTP |
-Related structure data
Related structure data | 27136MC 8d1eC 8d1fC 8d1gC 8d1hC 8d1iC 8d1jC 8d1kC 8d1lC 8d1mC 8d1oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 5 molecules EDACB
#1: Protein | Mass: 40408.918 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: BEST2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: E1BF86 |
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-Non-polymers , 5 types, 661 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-MC3 / #4: Chemical | ChemComp-DU0 / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: bBest2_345 Ca2+-bound open state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.210 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293F | ||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: bBest2_345 Ca2+-bound open state | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 3203 |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1070653 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 1.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117555 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6VX7 Accession code: 6VX7 / Source name: PDB / Type: experimental model |