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

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Basic information

Entry
Database: PDB / ID: 5wbx
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) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / alpha-actinin binding / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / voltage-gated potassium channel complex / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / potassium ion transport / Stimuli-sensing channels / Z disc / cellular response to type II interferon / 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 / Inactivation, recovery and regulation of the phototransduction cascade
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-AJY / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 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)28,56411
Polymers27,6602
Non-polymers9049
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-82 kcal/mol
Surface area15520 Å2
MethodPISA
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)57,12822
Polymers55,3214
Non-polymers1,80718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15190 Å2
ΔGint-230 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.328, 66.091, 65.435
Angle α, β, γ (deg.)90.000, 93.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-671-

HOH

21R-1180-

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, 227 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / 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-AJY / (3Z)-6-bromo-3-(hydroxyimino)-5-methyl-1,3-dihydro-2H-indol-2-one


Mass: 255.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7BrN2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M Sodium itrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Lithium 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: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3148 Å / Relative weight: 1
ReflectionResolution: 1.9→26.84 Å / Num. obs: 25882 / % possible obs: 98.4 % / Redundancy: 6.4 % / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
REFMACrefinement
XPREPdata scaling
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHASERphasing
RefinementResolution: 1.9→26.836 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.02
RfactorNum. reflection% reflection
Rfree0.2428 1192 4.77 %
Rwork0.1881 --
obs0.1907 24970 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.93 Å2 / Biso mean: 32.6831 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 1.9→26.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 48 218 2197
Biso mean--56.15 38.69 -
Num. residues----241
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)
13.0915-1.21870.81574.9970.71334.823-0.04130.33980.1762-0.1735-0.03520.1208-0.128-0.0575-0.04680.2352-0.0420.02440.18270.06140.131410.31858.1127-15.3544
21.03650.3136-0.9651.1647-1.31641.877-0.09390.13930.7152-0.36710.05190.5749-0.3735-0.07850.09420.54060.0221-0.15770.71870.05960.7586-8.63630.9067-10.3766
32.3609-0.1929-0.6641.54360.02512.339-0.0226-0.1842-0.29740.1240.09780.2636-0.0879-0.1018-0.05880.13460.04120.00920.17630.03740.189-23.48712.3269.1265
42.9309-0.2622-2.5460.56050.16643.7384-0.0588-0.1053-0.0012-0.02210.07670.05-0.09170.0897-0.04870.1222-0.0076-0.02480.11350.01930.1087-5.9987-0.6446-0.2993
50.4454-0.09180.10990.42330.18231.3057-0.16690.16810.0515-0.38760.1002-0.0815-0.25740.0261-0.19360.5905-0.23970.05840.4169-0.0980.13587.6999-5.8442-27.3653
61.2859-0.00540.48250.68080.17471.4951-0.44240.37260.1679-0.46840.33110.04680.1079-0.1445-0.02480.2281-0.1078-0.01040.21030.02390.14960.7286-11.4485-15.1063
70.24610.1510.111.1062-0.15410.3053-0.08730.05670.08250.06140.04820.05060.0311-0.1204-0.23960.5231-0.2836-0.20570.49040.30460.32080.5071-1.5851-25.054
83.0965-0.36983.55151.1043-0.515.4575-0.2283-0.11440.2891-0.18260.14710.0023-0.2807-0.42430.06790.185-0.02920.00310.16580.00990.182414.27219.4179-5.7335
91.3436-0.2236-0.03562.83770.85191.36240.2505-0.13-0.34820.3454-0.028-0.31480.29490.1236-0.1890.1528-0.0085-0.06060.1792-0.02440.265628.05683.59272.7279
103.7934-2.140.36769.0490.8752.14570.14350.233-0.5673-0.26940.1559-0.53130.02980.2614-0.0620.1564-0.06430.0090.2312-0.0860.410934.78896.1437-6.6979
112.6271.10711.11841.51640.79512.5695-0.08210.18010.323-0.30490.12360.1368-0.11790.0618-0.0690.1782-0.01820.00110.14290.00880.212126.454515.5806-2.7439
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 414 )B405 - 414
3X-RAY DIFFRACTION3chain 'B' and (resid 415 through 445 )B415 - 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 64 )R29 - 64
7X-RAY DIFFRACTION7chain 'R' and (resid 65 through 75 )R65 - 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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