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- PDB-4j9y: Calcium-calmodulin complexed with the calmodulin binding domain f... -

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Basic information

Entry
Database: PDB / ID: 4j9y
TitleCalcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant
Components
  • Calmodulin
  • Small conductance calcium-activated potassium channel protein 2
KeywordsTRANSPORT PROTEIN/CALCIUM BINDING / Calcium binding / EF hand / SK2a channel fragment / TRANSPORT PROTEIN-CALCIUM BINDING complex
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / regulation of store-operated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of high voltage-gated calcium channel activity / calcium-activated potassium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / 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 / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / smooth endoplasmic reticulum / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / T-tubule / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / potassium ion transport / modulation of chemical synaptic transmission / spindle microtubule / sarcolemma / Z disc / cellular response to type II interferon / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / postsynaptic membrane / vesicle / transmembrane transporter binding / protein autophosphorylation / dendritic spine / calmodulin binding / neuron projection / positive regulation of apoptotic process / 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 / nucleus / plasma membrane
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 / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsZhang, M. / Pascal, J.M. / Zhang, J.-F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Unstructured to structured transition of an intrinsically disordered protein peptide in coupling Ca2+-sensing and SK channel activation.
Authors: Zhang, M. / Pascal, J.M. / Zhang, J.F.
History
DepositionFeb 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Feb 28, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5568
Polymers29,0962
Non-polymers4606
Water5,783321
1
B: Small conductance calcium-activated potassium channel protein 2
R: Calmodulin
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)59,11316
Polymers58,1924
Non-polymers92112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14750 Å2
ΔGint-199 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.630, 66.820, 64.830
Angle α, β, γ (deg.)90.000, 94.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-623-

HOH

21R-1221-

HOH

31R-1227-

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 / SK2a / SK2 / SKCa 2 / SKCa2 / KCa2.2


Mass: 12243.395 Da / Num. of mol.: 1 / Fragment: Calmodulin Binding Domain (UNP residues 396-487)
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 / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS

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Non-polymers , 4 types, 327 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.51→38.879 Å / Num. all: 49769 / Num. obs: 49769 / % possible obs: 96.3 % / Redundancy: 5.3 % / Rsym value: 0.035 / Net I/σ(I): 24.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.51-1.555.30.6821.11914635950.68294
1.55-1.595.30.5421.41854034910.54294.5
1.59-1.645.30.4031.91823434180.40394.7
1.64-1.695.30.332.41763933200.3395.1
1.69-1.745.30.25931718532410.25995.4
1.74-1.85.30.19341679231660.19395.5
1.8-1.875.30.155.21610530410.1596.6
1.87-1.955.30.1067.41564729550.10696.1
1.95-2.045.30.07410.61500528510.07496.8
2.04-2.145.20.055141426327240.05597.2
2.14-2.255.20.044171361026020.04497.6
2.25-2.395.20.03619.81289224710.03697.7
2.39-2.555.20.03320.41208623350.03398
2.55-2.765.20.0322.61133821940.0398.4
2.76-3.025.10.02724.71036020240.02798.7
3.02-3.385.10.02229.1923218230.02298.5
3.38-3.95.20.01934.1843416160.01999.1
3.9-4.785.20.01640.3708913590.01698.4
4.78-6.755.20.01738.8552510700.01798.9
6.75-38.8794.70.01836.122154730.01878.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→38.879 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8573 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 2519 5.06 %
Rwork0.1827 --
obs0.1844 49765 96 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.985 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 88.11 Å2 / Biso mean: 30.2014 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1--5.1467 Å20 Å2-3.8131 Å2
2--5.8846 Å20 Å2
3----0.7379 Å2
Refinement stepCycle: LAST / Resolution: 1.51→38.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1874 0 23 321 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111956
X-RAY DIFFRACTIONf_angle_d1.2892630
X-RAY DIFFRACTIONf_chiral_restr0.075295
X-RAY DIFFRACTIONf_plane_restr0.006343
X-RAY DIFFRACTIONf_dihedral_angle_d12.892768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.5390.36051580.31272502266094
1.539-1.57050.31461430.28132562270594
1.5705-1.60460.27641500.24882576272695
1.6046-1.64190.26931480.24552543269194
1.6419-1.6830.24311570.23182541269895
1.683-1.72850.30931350.2392603273895
1.7285-1.77940.23941300.21682604273495
1.7794-1.83680.21111340.20862641277596
1.8368-1.90240.25331190.19332657277696
1.9024-1.97860.21541580.18042595275396
1.9786-2.06870.19671360.17332640277697
2.0687-2.17770.20241100.16472671278197
2.1777-2.31410.20131540.1652650280497
2.3141-2.49280.18781510.15942673282498
2.4928-2.74360.19611360.16092696283298
2.7436-3.14040.22571140.17162726284098
3.1404-3.9560.21411440.16892731287599
3.956-38.89230.19881420.18862635277794
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)
15.631-6.2119-1.31977.21390.55292.6903-0.2581-0.36070.81370.12660.2117-0.77450.03880.1782-0.08280.21160.0583-0.02650.2115-0.06110.203327.323163.756447.0325
24.54670.2146-1.05274.9118-1.12766.3071-0.10780.2812-0.3548-0.02360.0971-0.1720.22050.10860.01940.0979-0.0319-0.00760.1149-0.03140.158259.59459.313924.1303
37.01290.421-6.374-0.0035-0.32196.2986-0.07520.00240.04150.0170.0883-0.0535-0.0547-0.0265-0.02450.14850.0087-0.01310.1319-0.01180.13341.199856.440733.9688
41.32880.25570.60581.3186-0.34044.4011-0.2268-0.33790.23030.44030.02050.1333-0.488-0.5179-0.02930.51990.24570.0070.570.0699-0.001328.282850.843959.3084
52.7843-0.2961.06051.9485-0.8927.0998-0.3012-0.42950.15870.46860.141-0.2057-0.07380.25510.14150.20590.0696-0.01350.1254-0.02210.128235.20645.751647.124
62.5765-1.37673.10962.0096-2.30574.4482-0.10480.14560.39430.34040.0665-0.5269-0.16420.69290.37640.17090.1016-0.09550.2303-0.09890.192527.225762.189644.3689
71.1838-0.83680.86874.5646-1.55861.80660.17190.0124-0.5571-0.13660.13680.43090.2458-0.1093-0.25070.12840.002-0.04630.12220.01210.27195.533563.55732.213
84.7057-1.3863.74183.1808-1.60943.7339-0.3688-0.28060.63840.32770.1301-0.4346-0.654-0.14280.24990.1820.0428-0.01860.1088-0.03860.243112.572172.410336.3526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resseq 395:413)B395 - 413
2X-RAY DIFFRACTION2chain 'B' and (resseq 414:445)B414 - 445
3X-RAY DIFFRACTION3chain 'B' and (resseq 446:491)B446 - 491
4X-RAY DIFFRACTION4chain 'R' and (resseq 2:28)R2 - 28
5X-RAY DIFFRACTION5chain 'R' and (resseq 29:64)R29 - 64
6X-RAY DIFFRACTION6chain 'R' and (resseq 65:92)R65 - 92
7X-RAY DIFFRACTION7chain 'R' and (resseq 93:134)R93 - 134
8X-RAY DIFFRACTION8chain 'R' and (resseq 135:147)R135 - 147

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