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- EMDB-8410: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8410
TitleCa2+ bound aplysia Slo1
Map data
SampleCa2+ bound aplysia Slo1
  • High conductance calcium-activated potassium channel
  • (ligand) x 4
Function / homologyCalcium-activated potassium channel BK, alpha subunit / Ion transport domain / Calcium-activated potassium channel Slo-1 / Voltage-dependent channel domain superfamily / NAD(P)-binding domain superfamily / large conductance calcium-activated potassium channel activity / integral component of membrane / High conductance calcium-activated potassium channel
Function and homology information
Biological speciesAplysia californica (California sea hare)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMacKinnon R / Tao X / Hite RK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structure of the open high-conductance Ca-activated K channel.
Authors: Xiao Tao / Richard K Hite / Roderick MacKinnon /
Abstract: The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to ...The Ca-activated K channel, Slo1, has an unusually large conductance and contains a voltage sensor and multiple chemical sensors. Dual activation by membrane voltage and Ca renders Slo1 central to processes that couple electrical signalling to Ca-mediated events such as muscle contraction and neuronal excitability. Here we present the cryo-electron microscopy structure of a full-length Slo1 channel from Aplysia californica in the presence of Ca and Mg at a resolution of 3.5 Å. The channel adopts an open conformation. Its voltage-sensor domain adopts a non-domain-swapped attachment to the pore and contacts the cytoplasmic Ca-binding domain from a neighbouring subunit. Unique structural features of the Slo1 voltage sensor suggest that it undergoes different conformational changes than other known voltage sensors. The structure reveals the molecular details of three distinct divalent cation-binding sites identified through electrophysiological studies of mutant Slo1 channels.
Validation ReportPDB-ID: 5tj6

SummaryFull reportAbout validation report
History
DepositionOct 3, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseJan 11, 2017-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tj6
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8410.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 332.8 Å
1.3 Å/pix.
x 256 pix.
= 332.8 Å
1.3 Å/pix.
x 256 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.018576425 - 0.049764723
Average (Standard dev.)-0.00023435285 (±0.002291491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0190.050-0.000

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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: 6

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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, POTASSIUM ION

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

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Component #4: ligand, MAGNESIUM ION

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

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Component #5: ligand, CALCIUM ION

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

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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

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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: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
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: 2000 / Sampling size: 5 µm

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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

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL / Overall bvalue: 100
Output model

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