+Open data
-Basic information
Entry | Database: PDB / ID: 5tj6 | |||||||||
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Title | Ca2+ bound aplysia Slo1 | |||||||||
Components | High conductance calcium-activated potassium channel | |||||||||
Keywords | MEMBRANE PROTEIN / ion channel / K+ channel / Ca2+ bound / high conductance | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aplysia californica (California sea hare) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | MacKinnon, R. / Tao, X. / Hite, R.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2017 Title: Cryo-EM structure of the open high-conductance Ca-activated K channel. Authors: Xiao Tao / Richard K Hite / Roderick MacKinnon / Abstract: The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to ...The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to processes that couple electrical signalling to Ca-mediated events such as muscle contraction and neuronal excitability. Here we present the cryo-electron microscopy structure of a full-length Slo1 channel from Aplysia californica in the presence of Ca and Mg at a resolution of 3.5 Å. The channel adopts an open conformation. Its voltage-sensor domain adopts a non-domain-swapped attachment to the pore and contacts the cytoplasmic Ca-binding domain from a neighbouring subunit. Unique structural features of the Slo1 voltage sensor suggest that it undergoes different conformational changes than other known voltage sensors. The structure reveals the molecular details of three distinct divalent cation-binding sites identified through electrophysiological studies of mutant Slo1 channels. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5tj6.cif.gz | 204.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tj6.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/5tj6 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tj6 | HTTPS FTP |
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-Related structure data
Related structure data | 8410MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: C (n fold cyclic)) |
-Components
#1: Protein | Mass: 120308.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5QJC5 | ||||||
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#2: Chemical | ChemComp-K / #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Chemical | ChemComp-PGW / ( |
-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: Ca2+ bound aplysia Slo1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.4 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Aplysia californica (California sea hare) | |||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: High Five / Plasmid: pFastBac | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.3 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2000 |
Image scans | Sampling size: 5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 50 / Used frames/image: 1-50 |
-Processing
Software | Name: REFMAC / Version: 5.8.0088 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 233000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115000 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 100 / Protocol: AB INITIO MODEL / Space: RECIPROCAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.5→3.5 Å / Cor.coef. Fo:Fc: 0.85 / SU B: 39.858 / SU ML: 0.48 / ESU R: 1.568 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 291.609 Å2
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Refinement step | Cycle: 1 / Total: 7212 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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