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- PDB-5tji: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: PDB / ID: 5tji
TitleCa2+ bound aplysia Slo1
DescriptorHigh conductance calcium-activated potassium channel
KeywordsMEMBRANE PROTEIN / ion channel / K+ channel / Ca2+ bound / high conductance
Specimen sourceAplysia californica / invertebrata / California sea hare / image: Aplysia kurodai
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsMacKinnon, R. / Tao, X. / Hite, R.K.
CitationNature, 2017, 541, 52-57

Nature, 2017, 541, 52-57 StrPapers
Structural basis for gating the high-conductance Ca(2+)-activated K(+) channel.
Richard K Hite / Xiao Tao / Roderick MacKinnon

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 4, 2016 / Release: Dec 28, 2016
RevisionDateData content typeGroupProviderType
1.0Dec 28, 2016Structure modelrepositoryInitial release
1.1Jan 11, 2017Structure modelDatabase references
1.2Jan 18, 2017Structure modelDatabase references

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Structure visualization

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  • Biological unit as tetrameric
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Assembly

Deposited unit
A: High conductance calcium-activated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,0572
Polyers120,3081
Non-polymers7491
Water0
#1
A: High conductance calcium-activated potassium channel
hetero molecules

A: High conductance calcium-activated potassium channel
hetero molecules

A: High conductance calcium-activated potassium channel
hetero molecules

A: High conductance calcium-activated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,2288
Polyers481,2324
Non-polymers2,9964
Water0
TypeNameSymmetry operationNumber
point symmetry operation4
Buried area (Å2)16490
ΔGint (kcal/M)-78
Surface area (Å2)157170

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Components

#1: Polypeptide(L)High conductance calcium-activated potassium channel


Mass: 120308.000 Da / Num. of mol.: 1
Source: (gene. exp.) Aplysia californica / invertebrata / image: Aplysia kurodai
References: UniProt: Q5QJC5

Cellular component

Molecular function

  • large conductance calcium-activated potassium channel activity (GO: 0060072)
#2: ChemicalChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL / phospholipid *YM


Mass: 749.007 Da / Num. of mol.: 1 / Formula: C40H77O10P

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Ca2+ bound aplysia Slo1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 0.4 deg. / Units: MEGADALTONS / Experimental flag: NO
Source (natural)Organism: Aplysia californica
Source (recombinant)Cell: High Five / Organism: Trichoplusia ni / Plasmid: pFastBac
Buffer solutionpH: 8
Buffer component
IDConc.Conc. unitsNameFormulaBuffer ID
120mMTrisTris1
2450mMKClKCl1
320mMDTTDTT1
42mMTCEPTCEP1
50.025%DDMDDM1
60.005%CHSCHS1
71mMEDTAEDTA1
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 293 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.3 sec. / Electron dose: 1.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 4000
EM imaging opticsEnergyfilter name: Gatan / Energyfilter upper: 15 eV / Energyfilter lower: -15 eV / Sph aberration corrector: FEI Cs corrector on Titan Krios
Image scansSampling size: 5 microns / Dimension width: 7420 / Dimension height: 7676 / Movie frames/image: 50 / Used frames/image: 1-50

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameCategoryImage processing IDImaging IDFitting ID
1RelionPARTICLE SELECTION1
2SerialEMIMAGE ACQUISITION1
4CTFFIND4CTF CORRECTION1
7CootMODEL FITTING1
9RelionINITIAL EULER ASSIGNMENT1
10FrealignFINAL EULER ASSIGNMENT1
11RelionCLASSIFICATION1
12FrealignRECONSTRUCTION1
13RefmacMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 638000
SymmetryPoint symmetry: C4
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000 / Symmetry type: POINT
Atomic model buildingOverall b value: 160 / Ref protocol: AB INITIO MODEL / Ref space: RECIPROCAL
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1380.679-2.890.000.00-2.890.005.780.889HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.384800.384803.80147.0026401100.0086.7531.0470.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 6930
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0197095
ELECTRON MICROSCOPYr_bond_other_d0.0010.0206734
ELECTRON MICROSCOPYr_angle_refined_deg0.8611.9539642
ELECTRON MICROSCOPYr_angle_other_deg0.7713.00015390
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.6325.000875
ELECTRON MICROSCOPYr_dihedral_angle_2_deg28.66323.431306
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.52715.0001135
ELECTRON MICROSCOPYr_dihedral_angle_4_deg9.18615.00038
ELECTRON MICROSCOPYr_chiral_restr0.0470.2001104
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0207990
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0201716
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.10238.0513521
ELECTRON MICROSCOPYr_mcbond_other8.10338.0503520
ELECTRON MICROSCOPYr_mcangle_it13.89957.0574389
ELECTRON MICROSCOPYr_mcangle_other13.89757.0584390
ELECTRON MICROSCOPYr_scbond_it8.98939.6573574
ELECTRON MICROSCOPYr_scbond_other8.98839.6563575
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.57658.9915254
ELECTRON MICROSCOPYr_long_range_B_refined23.4957821
ELECTRON MICROSCOPYr_long_range_B_other23.4937822
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.8 Å / R factor R work: 0.747 / Lowest resolution: 3.899 Å / Number reflection R free: 0 / Number reflection R work: 1938 / Total number of bins used: 20 / Percent reflection obs: 1

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