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- PDB-6ale: A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivit... -

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Basic information

Entry
Database: PDB / ID: 6ale
TitleA V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model
Components
  • Calmodulin-2
  • Small conductance calcium-activated potassium channel protein 2
KeywordsMETAL TRANSPORT / Calcium binding protein
Function / homology
Function and homology information


small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / regulation of store-operated calcium channel activity / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / : / establishment of protein localization to mitochondrial membrane ...small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / regulation of store-operated calcium channel activity / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / : / establishment of protein localization to mitochondrial membrane / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / alpha-actinin binding / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / calcium channel complex / activation of adenylate cyclase activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / regulation of cytokinesis / calcium-mediated signaling / positive regulation of nitric-oxide synthase activity / spindle microtubule / potassium ion transport / Z disc / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / transmembrane transporter binding / dendritic spine / calmodulin binding / neuron projection / protein domain specific binding / centrosome / neuronal cell body / calcium ion binding / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / EF-hand domain pair ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Helix Hairpins - #70 / Potassium channel domain / Ion channel / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1KP / Calmodulin-2 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNam, Y.W. / Zhang, M.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association13SDG16150007 United States
National Ataxia FoundationYI-SCA United States
CitationJournal: Sci Rep / Year: 2018
Title: A V-to-F substitution in SK2 channels causes Ca2+hypersensitivity and improves locomotion in a C. elegans ALS model.
Authors: Nam, Y.W. / Baskoylu, S.N. / Gazgalis, D. / Orfali, R. / Cui, M. / Hart, A.C. / Zhang, M.
History
DepositionAug 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,53910
Polymers27,7512
Non-polymers7888
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.653, 66.913, 64.712
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11R-1136-

HOH

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Components

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Protein , 2 types, 2 molecules BR

#1: Protein Small conductance calcium-activated potassium channel protein 2 / SKCa2 / KCa2.2


Mass: 11331.361 Da / Num. of mol.: 1 / Fragment: calmodulin binding domain (UNP residues 394-486)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNN2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2S1
#2: Protein Calmodulin-2 /


Mass: 16420.031 Da / Num. of mol.: 1 / Fragment: UNP residues 5-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm2, Cam2, Camb, CaMII / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP30

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Non-polymers , 5 types, 124 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1KP / (3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one


Mass: 231.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4Cl2N2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium Citrate Tribasic dehydrate 0.6 M Ammonium sulfate 1.4 M Lithium sulfate monohydrate
PH range: 5.6-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: CMOS / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.72 Å / Num. obs: 11420 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 29.76 Å2 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
XPREPdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHASESphasing
RefinementResolution: 2.5→24.193 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.4
RfactorNum. reflection% reflection
Rfree0.2551 548 4.8 %
Rwork0.188 --
obs0.1912 11410 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.69 Å2 / Biso mean: 45.481 Å2 / Biso min: 16.1 Å2
Refinement stepCycle: final / Resolution: 2.5→24.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 42 116 2096
Biso mean--100.74 40.2 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071996
X-RAY DIFFRACTIONf_angle_d1.1272676
X-RAY DIFFRACTIONf_chiral_restr0.051293
X-RAY DIFFRACTIONf_plane_restr0.004346
X-RAY DIFFRACTIONf_dihedral_angle_d21.1531218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.75130.33081400.237826762816
2.7513-3.14870.30231470.219927012848
3.1487-3.96420.27641310.180127202851
3.9642-24.19440.18841300.16327652895
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.53962.813-4.83092.3239-1.39633.4133-0.22521.50831.1125-0.61640.81210.2716-0.7791-0.1663-0.13670.5279-0.2274-0.00150.48710.04820.35848.558.239417.0194
23.8586-0.5448-4.00910.07920.56924.17030.8173-0.46562.39480.4431-0.25481.1888-0.6715-0.9767-0.70721.00430.23730.10521.1174-0.21051.2918-10.7091.650921.6228
35.124-0.6741-1.93754.59780.66526.3568-0.2163-0.4718-0.54850.1016-0.03030.3038-0.2181-0.23550.31020.17780.0365-0.010.29850.08410.2297-24.60662.473140.8047
45.8499-1.2388-4.41871.09291.3066.7937-0.1084-0.4244-0.2816-0.0040.06880.0964-0.21850.4213-0.09160.212-0.0245-0.04260.20970.04490.2144-7.3369-0.44932.0194
52.17610.2002-1.08811.4123-0.93742.9728-0.54650.44110.1959-1.78110.5344-0.2904-0.20190.11650.25380.9753-0.39750.04350.67750.02380.28165.6319-5.75395.101
62.27760.4015-0.12891.4808-1.1911.7757-0.6840.72710.6766-1.07910.67290.37310.0225-0.23410.09720.5926-0.2114-0.10130.42730.11090.4197-1.04-9.129814.9138
77.8576-0.31815.39694.2425-1.21964.0411-0.5191-0.05410.5542-0.35310.50650.5275-0.5978-0.34470.2170.2968-0.06090.00750.31310.03830.312811.76799.281226.1004
85.52180.68380.36037.71640.24412.03080.03350.0644-0.51870.03380.1052-0.68620.08270.2744-0.11240.1802-0.0415-0.01480.3147-0.0360.287829.02956.484832.0028
96.62763.03144.07353.13982.19542.5704-0.34780.44170.5813-0.10520.22020.6527-0.35750.00350.18640.2674-0.0577-0.00770.24990.04280.361622.074415.344928.4218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 395 through 404 )B395 - 404
2X-RAY DIFFRACTION2chain 'B' and (resid 405 through 413 )B405 - 413
3X-RAY DIFFRACTION3chain 'B' and (resid 414 through 445 )B414 - 445
4X-RAY DIFFRACTION4chain 'B' and (resid 446 through 489 )B446 - 489
5X-RAY DIFFRACTION5chain 'R' and (resid 2 through 28 )R2 - 28
6X-RAY DIFFRACTION6chain 'R' and (resid 29 through 74 )R29 - 74
7X-RAY DIFFRACTION7chain 'R' and (resid 75 through 92 )R75 - 92
8X-RAY DIFFRACTION8chain 'R' and (resid 93 through 134 )R93 - 134
9X-RAY DIFFRACTION9chain 'R' and (resid 135 through 147 )R135 - 147

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