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- PDB-5wc5: Structural insights into the potency of SK/IK channel positive mo... -

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Basic information

Entry
Database: PDB / ID: 5wc5
TitleStructural insights into the potency of SK/IK channel positive modulators
Components
  • Calmodulin-1
  • 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 / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / Ca2+ activated K+ channels / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / inward rectifier potassium channel activity / regulation of potassium ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / potassium ion transmembrane transport / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / potassium ion transport / Stimuli-sensing channels / cellular response to type II interferon / Z disc / spindle pole / response to calcium ion / RAS processing / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium-dependent protein binding
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 / : ...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
7-fluoro-3-(hydroxyamino)-2H-indol-2-one / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 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: 2017
Title: Structural insights into the potency of SK channel positive modulators.
Authors: Nam, Y.W. / Orfali, R. / Liu, T. / Yu, K. / Cui, M. / Wulff, H. / Zhang, M.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,58912
Polymers27,6602
Non-polymers92910
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-1
hetero molecules

B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17824
Polymers55,3214
Non-polymers1,85820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15810 Å2
ΔGint-276 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.994, 66.015, 65.298
Angle α, β, γ (deg.)90.000, 93.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-639-

HOH

21B-657-

HOH

Detailsequilibrium centrifugation

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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: 11240.293 Da / Num. of mol.: 1 / Mutation: N407A
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-1


Mass: 16420.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23

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Non-polymers , 5 types, 185 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-AJV / 7-fluoro-3-(hydroxyamino)-2H-indol-2-one


Mass: 180.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5FN2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Litium sulfate monohydrate
PH range: 5.6-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.3148 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3148 Å / Relative weight: 1
ReflectionResolution: 2.1→26.76 Å / Num. obs: 18443 / % possible obs: 97.8 % / Redundancy: 6 % / Biso Wilson estimate: 22.77 Å2 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XPREPdata scaling
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHASERphasing
RefinementResolution: 2.3→26.788 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 721 4.97 %
Rwork0.195 13786 -
obs0.1978 14507 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.13 Å2 / Biso mean: 34.7876 Å2 / Biso min: 0.61 Å2
Refinement stepCycle: final / Resolution: 2.3→26.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 51 175 2157
Biso mean--64.97 34.57 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081995
X-RAY DIFFRACTIONf_angle_d1.2162676
X-RAY DIFFRACTIONf_chiral_restr0.049294
X-RAY DIFFRACTIONf_plane_restr0.005344
X-RAY DIFFRACTIONf_dihedral_angle_d8.0861215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.47750.37591270.27282732285999
2.4775-2.72660.32471390.25942764290399
2.7266-3.12060.31141380.21327552893100
3.1206-3.92970.21351400.16672763290399
3.9297-26.79010.19971770.15872772294999
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)
10.7547-1.75330.55874.65490.13893.9874-0.13410.53070.3258-0.22580.14540.1527-0.248-0.024-0.0940.2777-0.06780.02690.23330.05340.17988.11068.507817.2259
20.81140.4094-1.50580.4549-0.88612.8523-0.08590.47780.4806-0.68310.17210.5173-0.0346-0.2-0.09450.65270.0587-0.1880.5769-0.06570.7087-11.29490.094422.4304
32.1081-0.0679-0.3151.5451-0.28911.76240.0446-0.204-0.25270.05460.02190.3674-0.1274-0.1151-0.07170.12140.0538-0.00020.15940.03670.1895-25.99533.210942.0696
42.4633-0.396-1.54830.62910.32962.7678-0.0415-0.0717-0.0637-0.03850.07070.081-0.16690.0633-0.04250.1337-0.006-0.02030.09950.00810.1352-8.1325-0.251432.2623
50.5217-0.11510.0210.07970.30251.7205-0.19320.19350.0903-0.55330.1886-0.1131-0.27260.1432-0.16510.641-0.30750.10110.441-0.07320.20185.517-5.41445.2008
62.49420.50940.03620.58480.37791.8237-0.39430.38560.0582-0.36770.2569-0.00230.0841-0.09920.09070.2091-0.06570.02250.15270.00010.1360.4033-11.011420.1839
70.29650.3875-0.64861.0968-1.13111.5567-0.2160.32540.23340.05590.20960.2264-0.0599-0.2183-0.4420.462-0.3437-0.12560.50660.27120.264-4.0536-5.02057.9371
83.7013-0.49153.67511.3524-0.66385.7964-0.2315-0.28690.2785-0.16570.13370.1073-0.2669-0.61980.05980.1692-0.0340.01350.16910.0180.143412.02239.758626.8597
91.50590.4504-0.25882.80771.55821.64190.3125-0.2375-0.39240.34260.05-0.4040.31470.14-0.22840.1787-0.0256-0.08740.2098-0.00830.313825.76644.019235.4041
103.2501-1.6260.16857.09930.8631.78720.16930.2269-0.8796-0.37330.0737-0.6889-0.00720.3628-0.15860.185-0.08020.02440.2161-0.06380.422232.48466.581926.0194
112.51262.3441.412.21121.09342.8779-0.18440.11050.4086-0.19270.08760.0937-0.33490.0010.05130.1668-0.01010.01660.115-0.02940.212624.156315.960929.8431
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 415 )B405 - 415
3X-RAY DIFFRACTION3chain 'B' and (resid 416 through 445 )B416 - 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 55 )R29 - 55
7X-RAY DIFFRACTION7chain 'R' and (resid 56 through 75 )R56 - 75
8X-RAY DIFFRACTION8chain 'R' and (resid 76 through 92 )R76 - 92
9X-RAY DIFFRACTION9chain 'R' and (resid 93 through 117 )R93 - 117
10X-RAY DIFFRACTION10chain 'R' and (resid 118 through 128 )R118 - 128
11X-RAY DIFFRACTION11chain 'R' and (resid 129 through 147 )R129 - 147

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