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- PDB-5a6f: Cryo-EM structure of the Slo2.2 Na-activated K channel -

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Basic information

Entry
Database: PDB / ID: 5a6f
TitleCryo-EM structure of the Slo2.2 Na-activated K channel
Components
  • GATING RING OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1
  • RCK2 ELABORATION OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1
KeywordsTRANSPORT / 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
: / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / Potassium channel domain / Ion channel
Similarity search - Domain/homology
Potassium channel subfamily T member 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHite, R.K. / Yuan, P. / Li, Z. / Hsuing, Y. / Walz, T. / MacKinnon, R.
CitationJournal: 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
DepositionJun 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Apr 13, 2016Group: Atomic model / Other
Revision 1.3Aug 30, 2017Group: Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3063
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Assembly

Deposited unit
C: GATING RING OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1
D: RCK2 ELABORATION OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1


Theoretical massNumber of molelcules
Total (without water)82,9992
Polymers82,9992
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein GATING RING OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1 / SEQUENCE LIKE A CALCIUM-ACTIVATED POTASSIUM CHANNEL SUBUNIT / SLO2.2


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
#2: Protein/peptide RCK2 ELABORATION OF POTASSIUM CHANNEL SUBFAMILY T MEMBER 1 / SEQUENCE LIKE A CALCIUM-ACTIVATED POTASSIUM CHANNEL SUBUNIT / SLO2.2


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 detailsTHE REGISTER OF THE RESIDUES OF CHAIN D SAMPLE SEQUENCE FOR THE ENTRY IS UNKNOWN. HENCE THEY ARE ...THE REGISTER OF THE RESIDUES OF CHAIN D SAMPLE SEQUENCE FOR THE ENTRY IS UNKNOWN. HENCE THEY ARE CHANGED TO UNK. THE SAMPLE SEQUENCE CORRESPONDS TO UNP Q8QFV0.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SLO2.2 / Type: COMPLEX
Buffer solutionName: 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)
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: 84 HUMIDITY 4 SECOND BLOT LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 2000

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Processing

CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.2 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-3063. (DEPOSITION ID: 13532).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor / Details: REFINEMENT PROTOCOL--EM
RefinementHighest resolution: 4.2 Å
Refinement stepCycle: LAST / Highest resolution: 4.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 0 0 4551

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