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- EMDB-8410: Ca2+ bound aplysia Slo1 -

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Basic information

Database: EMDB / ID: 8410
TitleCa2+ bound aplysia Slo1
SampleCa2+ bound aplysia Slo1
SourceAplysia californica / invertebrata / image: Aplysia kurodai
Map dataMg and Ca-bound aplysia Slo1
Methodsingle particle reconstruction, at 3.5 Å resolution
AuthorsMacKinnon R / Tao X
CitationNature, 2017, 541, 46-51

Nature, 2017, 541, 46-51 Yorodumi Papers
Cryo-EM structure of the open high-conductance Ca(2+)-activated K(+) channel.
Xiao Tao / Richard K Hite / Roderick MacKinnon

Validation ReportPDB-ID: 5tj6

SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2016 / Header (metadata) release: Nov 16, 2016 / Map release: Jan 11, 2017 / Last update: Sep 27, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tj6
  • Surface level: 0.014
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8410.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Contour Level:0.014 (by author), 0.014 (movie #1):
Minimum - Maximum-0.018576425 - 0.049764723
Average (Standard dev.)-0.00023435285 (0.002291491)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
start NX/NY/NZ-190-190-190
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0190.050-0.000

Supplemental data

Sample components

Entire Ca2+ bound aplysia Slo1

EntireName: Ca2+ bound aplysia Slo1 / Number of components: 6
MassTheoretical: 400 kDa

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

Cellular-componentName: Ca2+ bound aplysia Slo1 / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: Aplysia californica / invertebrata / image: Aplysia kurodai
Source (engineered)Expression System: Trichoplusia ni / arthropod / イラクサキンウワバ, イラクサギンウワバ
Vector: pFastBac / Cell of expression system: High Five

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

ProteinName: High conductance calcium-activated potassium channel / Recombinant expression: No
MassTheoretical: 120.308 kDa
Source (engineered)Expression System: Aplysia californica / invertebrata / image: Aplysia kurodai

Component #3: ligand, POTASSIUM ION

LigandName: POTASSIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

Component #5: ligand, CALCIUM ION

LigandName: CALCIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

Component #6: 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: 15 / Recombinant expression: No
MassTheoretical: 0.749007 kDa

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 7 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 85 %

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: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
CameraDetector: GATAN K2 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2000 / Sampling size: 5 microns

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 115000
3D reconstructionSoftware: FREALIGN / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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