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

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Basic information

Entry
Database: PDB / ID: 6czq
TitleA V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model
Components
  • Calmodulin-1
  • Small conductance calcium-activated potassium channel protein 2
KeywordsMETAL TRANSPORT / Calcium binding protein
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / establishment of protein localization to mitochondrial membrane / positive regulation of potassium ion transport / inward rectifier potassium channel activity / type 3 metabotropic glutamate receptor binding / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / establishment of protein localization to mitochondrial membrane / positive regulation of potassium ion transport / inward rectifier potassium channel activity / type 3 metabotropic glutamate receptor binding / regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / regulation of neuronal synaptic plasticity / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / alpha-actinin binding / protein phosphatase activator activity / smooth endoplasmic reticulum / calcium channel regulator 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 / cellular response to interferon-beta / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / T-tubule / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / calcium-mediated signaling / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / sarcolemma / modulation of chemical synaptic transmission / potassium ion transport / Z disc / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / postsynaptic membrane / transmembrane transporter binding / dendritic spine / calmodulin binding / protein domain specific binding / centrosome / neuronal cell body / glutamatergic synapse / calcium ion binding / protein kinase binding / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol / 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
Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNam, Y.W. / Zhang, M.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association13SDG16150007 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1 R21 NS101182-01A1 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
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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)28,1207
Polymers27,7512
Non-polymers3685
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-81 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.273, 66.726, 64.676
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-619-

HOH

21B-643-

HOH

31R-1159-

HOH

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Components

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


Mass: 11331.361 Da / Num. of mol.: 1 / Fragment: residues 395-487 / Mutation: A395G, V407F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnn2 / Production host: Escherichia coli (E. coli) / References: UniProt: P70604
#2: Protein Calmodulin-1 /


Mass: 16420.031 Da / Num. of mol.: 1 / Fragment: residues 5-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calm1, Calm, Cam, Cam1, CaMI / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP29
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3148 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Aug 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3148 Å / Relative weight: 1
ReflectionResolution: 2.2→26.866 Å / Num. obs: 16535 / % possible obs: 99.75 % / Redundancy: 6.71 % / Biso Wilson estimate: 25.59 Å2 / Net I/σ(I): 14.44
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1618 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
APEX 2data scaling
PDB_EXTRACT3.24data extraction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→26.866 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.03
RfactorNum. reflection% reflection
Rfree0.2493 916 5.54 %
Rwork0.1977 --
obs0.2007 16535 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.47 Å2 / Biso mean: 43.1776 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: final / Resolution: 2.2→26.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 17 132 2087
Biso mean--84.52 42.5 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081972
X-RAY DIFFRACTIONf_angle_d0.8552643
X-RAY DIFFRACTIONf_chiral_restr0.049293
X-RAY DIFFRACTIONf_plane_restr0.005345
X-RAY DIFFRACTIONf_dihedral_angle_d9.4111216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.3160.2871350.231222222357100
2.316-2.4610.30071150.215122102325100
2.461-2.65090.3171100.228822532363100
2.6509-2.91730.25791410.213721962337100
2.9173-3.33880.2861220.200322622384100
3.3388-4.2040.22381590.17282209236899
4.204-26.86810.21441340.186622672401100
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)
17.6062-1.99160.23348.16840.52326.1768-0.10831.01640.2541-0.72920.21380.1456-0.3869-0.1792-0.10890.3365-0.06830.01470.36150.10150.2078.54818.372116.9846
22.589-0.0598-1.51963.7808-3.03873.391-0.0350.43090.6323-0.28030.0430.5977-0.3011-0.1687-0.01440.88080.1544-0.3221.05030.06751.1408-10.08881.723221.4388
33.6321-0.0581-1.01192.83980.15883.0769-0.1549-0.3377-0.44370.3070.18620.29160.0268-0.29480.03880.14630.08030.01460.24140.06630.2049-24.27432.550140.9833
45.9063-0.7736-4.96731.04730.65217.3415-0.1369-0.1251-0.2087-0.01620.08210.0451-0.18980.0957-0.05010.1211-0.0158-0.05440.12140.03010.1628-7.1894-0.268632.0437
51.37170.0332-0.87120.3453-0.28753.4309-0.30520.18010.0997-0.94670.1507-0.1835-0.2220.28560.05420.9176-0.4520.07250.59460.00780.18595.6399-5.59265.0348
62.15831.32210.08682.85190.3052.2793-0.64280.93960.4355-0.95210.70760.30240.0939-0.1592-0.08090.3442-0.1888-0.02320.33770.05310.2638-0.8167-11.181617.2989
70.96391.3692-0.00772.3515-0.37990.6458-0.22970.16550.0909-0.30960.09070.12160.1447-0.0929-0.34130.7427-0.4637-0.28810.56210.43080.5917-1.256-1.45517.7168
85.0742-0.06794.59252.9145-0.10425.9978-0.4066-0.22680.4824-0.29680.39930.4396-0.6034-0.50890.11140.2089-0.05030.03680.23680.03030.218212.49829.653326.8552
92.7333-0.0659-0.0844.15370.61931.8890.1386-0.2348-0.35830.35830.0818-0.31270.07590.2484-0.16710.1582-0.0492-0.00460.2513-0.00370.262226.41694.113634.8629
105.335-2.31710.62311.62770.31694.2972-0.05460.373-0.4315-0.2240.2849-0.8735-0.10350.7277-0.14750.2397-0.10420.03280.3564-0.0790.447533.06056.824525.5325
114.42672.25412.55882.29431.67654.409-0.29320.32110.483-0.14390.22120.1725-0.39480.24970.00430.2181-0.0507-0.00520.20310.00940.315724.733516.00429.5446
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 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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