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- EMDB-8414: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: EMDB / ID: 8414
TitleCa2+ bound aplysia Slo1
Map dataAplysia Slo1 in 1 mM EDTA
SampleCa2+ bound aplysia Slo1
  • High conductance calcium-activated potassium channel
  • ligand
Function / homologyPotassium channel, BK, alpha subunit / Ion transport domain / Calcium-activated potassium channel Slo-1 / Voltage-dependent channel domain superfamily / NAD(P)-binding domain superfamily / Ion transport protein / Calcium-activated BK potassium channel alpha subunit / large conductance calcium-activated potassium channel activity / integral component of membrane / metal ion binding / High conductance calcium-activated potassium channel
Function and homology information
SourceAplysia californica (California sea hare)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsMacKinnon R / Tao X / Hite RK
CitationJournal: Nature / Year: 2017
Title: Structural basis for gating the high-conductance Ca-activated K channel.
Authors: Richard K Hite / Xiao Tao / Roderick MacKinnon
Validation ReportPDB-ID: 5tji

SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2016 / Header (metadata) release: Nov 16, 2016 / Map release: Dec 28, 2016 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tji
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8414.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å
256 pix
1.35 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.036365576 - 0.204226
Average (Standard dev.)0.0031882646 (0.01626475)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0360.2040.003

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Supplemental data

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Sample components

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Entire Ca2+ bound aplysia Slo1

EntireName: Ca2+ bound aplysia Slo1 / Number of components: 3

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Component #1: cellular-component, Ca2+ bound aplysia Slo1

Cellular-componentName: Ca2+ bound aplysia Slo1 / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: Aplysia californica (California sea hare)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper) / Vector: pFastBac / Cell of expression system: High Five

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Component #2: protein, High conductance calcium-activated potassium channel

ProteinName: High conductance calcium-activated potassium channel / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 120.308 kDa
SourceSpecies: Aplysia californica (California sea hare)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: ligand, (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phos...

LigandName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.749007 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 7 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 85 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm / Energy filter: GIF / Energy window: -15-15 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4000 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 60000
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL / Overall bvalue: 16
Output model

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