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- EMDB-7558: MicroED structure of NaK ion channel reveals a process of Na+ par... -

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Basic information

Entry
Database: EMDB / ID: EMD-7558
TitleMicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter
Map dataNaK ion channel
Sample
  • Complex: NaK
    • Protein or peptide: Potassium channel protein
    • Ligand: SODIUM ION
  • Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL
  • Ligand: water
Keywordsion channel / NaK / TRANSPORT PROTEIN
Function / homologyTwo pore domain potassium channel / Potassium channel domain / Ion channel / potassium channel activity / metal ion binding / identical protein binding / membrane / Transporter / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
Methodelectron crystallography / cryo EM / Resolution: 2.5002 Å
AuthorsLiu S / Gonen T
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)1 United States
CitationJournal: 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
DepositionMar 14, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseSep 12, 2018-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.143205
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.143205
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cpv
  • Surface level: 0.143205
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6cpv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7558.png

Downloads & links

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Map

FileDownload / File: emd_7558.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNaK ion channel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.53 Å/pix.
x 193 pix.
= 89.3 Å		0.52 Å/pix.
x 136 pix.
= 68.072 Å		0.52 Å/pix.
x 114 pix.
= 68.072 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 0.51569 Å / Y: 0.51569 Å / Z: 0.53155 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143205 / Movie #1: 0.143205
Minimum - Maximum-0.37587637 - 0.8617665
Average (Standard dev.)0.0000059192867 (±0.095471166)
SymmetrySpace group: 79
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-69-50-137
Dimensions136114193
Spacing132132168
CellA: 68.0716 Å / B: 68.0716 Å / C: 89.299995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.515696969696970.515696969696970.53154761904762
M x/y/z132132168
origin x/y/z0.0000.0000.000
length x/y/z68.07268.07289.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-50-137
NX/NY/NZ136114193
MAP C/R/S213
start NC/NR/NS-50-69-137
NC/NR/NS114136193
D min/max/mean-0.3760.8620.000

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Supplemental data

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Sample components

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Entire : NaK

EntireName: NaK
Components
  • Complex: NaK
    • Protein or peptide: Potassium channel protein
    • Ligand: SODIUM ION
  • Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL
  • Ligand: water

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Supramolecule #1: NaK

SupramoleculeName: NaK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus cereus (bacteria)

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Macromolecule #1: Potassium channel protein

MacromoleculeName: Potassium channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus cereus (bacteria)
Molecular weightTheoretical: 10.706538 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
WKDKEFQVLF VLTILTLISG TIFYSTVEGL RPIDALYFSV VTLTTVGDGN FSPQTDFGKI FTILYIFIGI GLVFGFIHKL AVNVQLPSI LSNLVPR

UniProtKB: Transporter

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 12
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: (4S)-2-METHYL-2,4-PENTANEDIOL

MacromoleculeName: (4S)-2-METHYL-2,4-PENTANEDIOL / type: ligand / ID: 3 / Number of copies: 1 / Formula: MPD
Molecular weightTheoretical: 118.174 Da
Chemical component information

ChemComp-MPD:
(4S)-2-METHYL-2,4-PENTANEDIOL / precipitant*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 1750 mm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5002 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Crystallography statisticsNumber 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

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Atomic model buiding 1

RefinementOverall B value: 41
Output model

PDB-6cpv:
MicroED structure of NaK ion channel reveals a process of Na+ partition into the selectivity filter

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