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- EMDB-8414: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8414
TitleCa2+ bound aplysia Slo1
Map data
SampleCa2+ bound aplysia Slo1
  • High conductance calcium-activated potassium channel
  • ligand
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: 3.8 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: Structural basis for gating the high-conductance Ca-activated K channel.
Authors: Richard K Hite / Xiao Tao / Roderick MacKinnon /
Abstract: The precise control of an ion channel gate by environmental stimuli is crucial for the fulfilment of its biological role. The gate in Slo1 K channels is regulated by two separate stimuli, ...The precise control of an ion channel gate by environmental stimuli is crucial for the fulfilment of its biological role. The gate in Slo1 K channels is regulated by two separate stimuli, intracellular Ca concentration and membrane voltage. Slo1 is thus central to understanding the relationship between intracellular Ca and membrane excitability. Here we present the Slo1 structure from Aplysia californica in the absence of Ca and compare it with the Ca-bound channel. We show that Ca binding at two unique binding sites per subunit stabilizes an expanded conformation of the Ca sensor gating ring. These conformational changes are propagated from the gating ring to the pore through covalent linkers and through protein interfaces formed between the gating ring and the voltage sensors. The gating ring and the voltage sensors are directly connected through these interfaces, which allow membrane voltage to regulate gating of the pore by influencing the Ca sensors.
Validation ReportPDB-ID: 5tji

SummaryFull reportAbout validation report
History
DepositionOct 4, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseDec 28, 2016-
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: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tji
  • Surface level: 0.11
  • 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_8414.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.)
1.35 Å/pix.
x 256 pix.
= 345.6 Å
1.35 Å/pix.
x 256 pix.
= 345.6 Å
1.35 Å/pix.
x 256 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 LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.036365576 - 0.204226
Average (Standard dev.)0.0031882646 (±0.01626475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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: 22500.0 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 µm

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Image processing

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

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Atomic model buiding

Modeling #1Refinement space: RECIPROCAL / Overall bvalue: 160
Output model

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