+Open data
-Basic information
Entry | Database: PDB / ID: 5a6e | |||||||||
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Title | Cryo-EM structure of the Slo2.2 Na-activated K channel | |||||||||
Components |
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Keywords | TRANSPORT / ION CHANNEL / POTASSIUM CHANNEL | |||||||||
Function / homology | Function and homology information intracellular sodium-activated potassium channel activity / outward rectifier potassium channel activity / potassium ion transmembrane transport / plasma membrane Similarity search - Function | |||||||||
Biological species | GALLUS GALLUS (chicken) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Hite, R.K. / Yuan, P. / Li, Z. / Hsuing, Y. / Walz, T. / MacKinnon, R. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Cryo-electron microscopy structure of the Slo2.2 Na(+)-activated K(+) channel. Authors: Richard K Hite / Peng Yuan / Zongli Li / Yichun Hsuing / Thomas Walz / Roderick MacKinnon / Abstract: Na(+)-activated K(+) channels are members of the Slo family of large conductance K(+) channels that are widely expressed in the brain, where their opening regulates neuronal excitability. These ...Na(+)-activated K(+) channels are members of the Slo family of large conductance K(+) channels that are widely expressed in the brain, where their opening regulates neuronal excitability. These channels fulfil a number of biological roles and have intriguing biophysical properties, including conductance levels that are ten times those of most other K(+) channels and gating sensitivity to intracellular Na(+). Here we present the structure of a complete Na(+)-activated K(+) channel, chicken Slo2.2, in the Na(+)-free state, determined by cryo-electron microscopy at a nominal resolution of 4.5 ångströms. The channel is composed of a large cytoplasmic gating ring, in which resides the Na(+)-binding site and a transmembrane domain that closely resembles voltage-gated K(+) channels. In the structure, the cytoplasmic domain adopts a closed conformation and the ion conduction pore is also closed. The structure reveals features that can explain the unusually high conductance of Slo channels and how contraction of the cytoplasmic gating ring closes the pore. | |||||||||
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 | 5a6e.cif.gz | 282.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a6e.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 5a6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a6e_validation.pdf.gz | 783.5 KB | Display | wwPDB validaton report |
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Full document | 5a6e_full_validation.pdf.gz | 791 KB | Display | |
Data in XML | 5a6e_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 5a6e_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/5a6e ftp://data.pdbj.org/pub/pdb/validation_reports/a6/5a6e | HTTPS FTP |
-Related structure data
Related structure data | 3062MC 3063C 3064C 5a6fC 5a6gC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 11847.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) |
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#2: Protein | Mass: 10715.890 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8QFV0 |
#3: Protein | Mass: 79321.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8QFV0 |
#4: Protein/peptide | Mass: 3677.524 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) |
Sequence details | THE REGISTER OF CHAINS A AND D OF THE SAMPLE SEQUENCE FOR THE ENTRY IS UNKNOWN. HENCE THEY ARE ...THE REGISTER OF CHAINS A AND D OF THE SAMPLE SEQUENCE FOR THE ENTRY IS UNKNOWN. HENCE THEY ARE CHANGED TO UNK. THE SAMPLE SEQUENCE CORRESPOND |
-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: SLO2.2 / Type: COMPLEX |
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Buffer solution | Name: 20 MM HEPES PH 7.4, 300MM KCL, 1.5 MM DODECYL MALTOSIDE, 0.05 MG/ML POPE/POPG (3/1) pH: 7.4 Details: 20 MM HEPES PH 7.4, 300MM KCL, 1.5 MM DODECYL MALTOSIDE, 0.05 MG/ML POPE/POPG (3/1) |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: PLUNGE FREEZE INTO LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 7, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
Image scans | Num. digital images: 2000 |
-Processing
CTF correction | Details: EACH IMAGE | ||||||||||||
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Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 4.5 Å / Num. of particles: 24231 / Nominal pixel size: 1.04 Å / Actual pixel size: 1.04 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3062 (DEPOSITION ID: 13529). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor / Details: METHOD--REFINEMENT REFINEMENT PROTOCOL--EM | ||||||||||||
Refinement | Highest resolution: 4.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.5 Å
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