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- PDB-5tj6: Ca2+ bound aplysia Slo1 -

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Basic information

Entry
Database: PDB / ID: 5tj6
TitleCa2+ bound aplysia Slo1
ComponentsHigh conductance calcium-activated potassium channel
KeywordsMEMBRANE PROTEIN / ion channel / K+ channel / Ca2+ bound / high conductance
Function / homologyPotassium channel, BK, alpha subunit / Ion transport domain / Calcium-activated potassium channel Slo-1 / Voltage-dependent channel domain superfamily / NAD(P)-binding domain superfamily / Ion transport protein / Calcium-activated BK potassium channel alpha subunit / large conductance calcium-activated potassium channel activity / integral component of membrane / High conductance calcium-activated potassium channel
Function and homology information
Specimen sourceAplysia californica (California sea hare)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsMacKinnon, R. / Tao, X. / Hite, R.K.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2016 / Release: Dec 14, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 14, 2016Structure modelrepositoryInitial release
1.1Jan 11, 2017Structure modelDatabase references
1.2Jan 18, 2017Structure modelDatabase references
1.3Sep 27, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization

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Structure visualization

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  • Biological unit as author_defined_assembly
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  • Deposited structure unit
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,84324
Polyers120,3081
Non-polymers11,53523
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)527,37296
Polyers481,2324
Non-polymers46,14092
Water0
TypeNameSymmetry operationNumber
point symmetry operation4

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Components

#1: Protein/peptide High conductance calcium-activated potassium channel


Mass: 120308.000 Da / Num. of mol.: 1
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5QJC5
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Formula: K / Potassium
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#5: Chemical
ChemComp-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


Mass: 749.007 Da / Num. of mol.: 15 / Formula: C40H77O10P / Phosphatidylglycerol / Comment: phospholipid *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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 MDa / Experimental value: NO
Source (natural)Organism: Aplysia californica (California sea hare)
Source (recombinant)Cell: High Five / Organism: Trichoplusia ni (cabbage looper) / Plasmid: pFastBac
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTrisTris1
2320 mMKClKCl1
310 mMCaCl2CaCl21
410 mMMgCl2MgCl21
520 mMDTTDTT1
62 mMTCEPTCEP1
70.025 %DDMDDM1
80.005 %CHSCHS1
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 FIELDBright-field microscopy / 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: 1.8 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: 2000
Image scansSampling size: 5 microns / Width: 7420 / 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
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10FREALIGNfinal Euler assignment
11RELIONclassification
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 233000
SymmetryPoint symmetry: C4
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 115000 / Symmetry type: POINT
Atomic model buildingOverall b value: 100 / 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 MLOverall ESU RSolvent ion probe radiiSolvent shrinkage radiiSolvent vdw probe radiiStereochemistry target valuesSolvent model details
1291.609-0.240.000.00-0.240.000.490.850HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.328000.328003.40141.0032498100.0039.8580.4801.5680.800.801.20MAXIMUM LIKELIHOOD WITH PHASESMASK
ELECTRON MICROSCOPY
Number of atoms included #1Total: 7212
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0197356
ELECTRON MICROSCOPYr_bond_other_d0.0010.0207068
ELECTRON MICROSCOPYr_angle_refined_deg0.9491.9699934
ELECTRON MICROSCOPYr_angle_other_deg0.8053.00016206
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.2665.000883
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.15323.653323
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.64415.0001178
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.38715.00040
ELECTRON MICROSCOPYr_chiral_restr0.0510.2001111
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0208139
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0201740
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_it3.68230.4593553
ELECTRON MICROSCOPYr_mcbond_other3.67830.4593552
ELECTRON MICROSCOPYr_mcangle_it6.41045.6864429
ELECTRON MICROSCOPYr_mcangle_other6.41045.6874430
ELECTRON MICROSCOPYr_scbond_it3.76631.1723803
ELECTRON MICROSCOPYr_scbond_other3.76631.1723804
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.89246.5715506
ELECTRON MICROSCOPYr_long_range_B_refined10.6097953
ELECTRON MICROSCOPYr_long_range_B_other10.6097954
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.4 Å / R factor R work: 0.789 / Lowest resolution: 3.488 Å / Number reflection R free: 0 / Number reflection R work: 2393 / Total number of bins used: 20 / Percent reflection obs: 1

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