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Yorodumi- EMDB-7558: MicroED structure of NaK ion channel reveals a process of Na+ par... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7558 | |||||||||
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Title | MicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter | |||||||||
Map data | NaK ion channel | |||||||||
Sample |
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Keywords | ion channel / NaK / TRANSPORT PROTEIN | |||||||||
Function / homology | Two pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / identical protein binding / membrane / metal ion binding / Transporter / Potassium channel protein Function and homology information | |||||||||
Biological species | Bacillus cereus (bacteria) | |||||||||
Method | electron crystallography / cryo EM / Resolution: 2.5002 Å | |||||||||
Authors | Liu S / Gonen T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2018 Title: MicroED structure of the NaK ion channel reveals a Na partition process into the selectivity filter. Authors: Shian Liu / Tamir Gonen / Abstract: Sodium (Na) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration ...Sodium (Na) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na are proposed to play critical roles in determining the conductance and the selectivity of Na channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na-conducting channel, NaK, to 2.5 Å resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na ion at the entrance of the channel pore. A process of dilation coupled with Na movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7558.map.gz | 10.3 MB | EMDB map data format | |
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Header (meta data) | emd-7558-v30.xml emd-7558.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_7558.png | 62.9 KB | ||
Filedesc metadata | emd-7558.cif.gz | 5.1 KB | ||
Filedesc structureFactors | emd_7558_sf.cif.gz | 509.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7558 | HTTPS FTP |
-Validation report
Summary document | emd_7558_validation.pdf.gz | 522 KB | Display | EMDB validaton report |
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Full document | emd_7558_full_validation.pdf.gz | 521.6 KB | Display | |
Data in XML | emd_7558_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_7558_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7558 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7558 | HTTPS FTP |
-Related structure data
Related structure data | 6cpvMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7558.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | NaK ion channel | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.51569 Å / Y: 0.51569 Å / Z: 0.53155 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 79 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : NaK
Entire | Name: NaK |
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Components |
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-Supramolecule #1: NaK
Supramolecule | Name: NaK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Bacillus cereus (bacteria) |
-Macromolecule #1: Potassium channel protein
Macromolecule | Name: Potassium channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus cereus (bacteria) |
Molecular weight | Theoretical: 10.706538 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: WKDKEFQVLF VLTILTLISG TIFYSTVEGL RPIDALYFSV VTLTTVGDGN FSPQTDFGKI FTILYIFIGI GLVFGFIHKL AVNVQLPSI LSNLVPR UniProtKB: Transporter |
-Macromolecule #2: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 2 / Number of copies: 12 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #3: (4S)-2-METHYL-2,4-PENTANEDIOL
Macromolecule | Name: (4S)-2-METHYL-2,4-PENTANEDIOL / type: ligand / ID: 3 / Number of copies: 1 / Formula: MPD |
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Molecular weight | Theoretical: 118.174 Da |
Chemical component information | ChemComp-MPD: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron crystallography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1750 mm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.5002 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystallography statistics | Number intensities measured: 27479 / Number structure factors: 5643 / Fourier space coverage: 81.7 / R sym: 0.206 / R merge: 0.206 / Overall phase error: 20.27 / Overall phase residual: 20.27 / Phase error rejection criteria: 0 / High resolution: 2.5002 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.5002 Å / Shell - Low resolution: 3.1486 Å / Shell - Number structure factors: 2685 / Shell - Phase residual: 22.68 / Shell - Fourier space coverage: 0.76 / Shell - Multiplicity: 4.1 |
-Atomic model buiding 1
Refinement | Overall B value: 41 |
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Output model | PDB-6cpv: |