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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 A resolution / 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

DateDeposition: Oct 4, 2016 / Release: Dec 28, 2016 / Last modification: Jan 18, 2017

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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 (A2)16490
ΔGint (kcal/M)-78
Surface area (A2)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
#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 experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Ca2+ bound aplysia Slo1 / Type: ORGANELLE OR CELLULAR COMPONENT
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85

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Electron microscopy imaging

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 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
EM image scansSampling size: 5 microns

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
ComputingStructure refinement: REFMAC 5.8.0088
3D reconstructionResolution: 3.8 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000
Atomic model buildingOverall b value: 160 / Ref protocol: AB INITIO MODEL / Ref space: RECIPROCAL
Refine

B iso mean: 380.679 A2 / Aniso B11: -2.89 A2 / Aniso B12: 0 A2 / Aniso B13: 0 A2 / Aniso B22: -2.89 A2 / Aniso B23: 0 A2 / Aniso B33: 5.78 A2 / Correlation coeff Fo to Fc: 0.889 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / R factor R work: 0.3848 / R factor obs: 0.3848 / Highest resolution: 3.8 A / Lowest resolution: 147 A / Number reflection obs: 26401 / Percent reflection obs: 1 / Overall SU B: 86.753 / Overall SU ML: 1.047 / Solvent ion probe radii: 0.8 A / Solvent shrinkage radii: 0.8 A / Solvent vdw probe radii: 1.2 A / Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES / Solvent model details: MASK

Refine id
1
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 A / R factor R work: 0.747 / Lowest resolution: 3.899 A / Number reflection R free: 0 / Number reflection R work: 1938 / Total number of bins used: 20 / Percent reflection obs: 1

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