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- PDB-4j9z: Calcium-calmodulin complexed with the calmodulin binding domain f... -

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Basic information

Entry
Database: PDB / ID: 4j9z
TitleCalcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant and NS309
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 / regulation of store-operated calcium channel activity / : / : / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : ...Ca2+ activated K+ channels / regulation of store-operated calcium channel activity / : / : / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / : / : / calcium-activated potassium channel activity / : / transporter inhibitor activity / positive regulation of potassium ion transport / : / inward rectifier potassium channel activity / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / response to corticosterone / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / smooth endoplasmic reticulum / alpha-actinin binding / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / regulation of neuronal synaptic plasticity / regulation of synaptic vesicle endocytosis / monoatomic ion channel activity / detection of calcium ion / postsynaptic cytosol / cell surface receptor signaling pathway via JAK-STAT / regulation of cardiac muscle contraction / catalytic complex / phosphatidylinositol 3-kinase binding / activation of adenylate cyclase activity / enzyme regulator activity / positive regulation of nitric-oxide synthase activity / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / regulation of calcium-mediated signaling / monoatomic ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / T-tubule / regulation of heart rate / calyx of Held / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / sarcomere / response to amphetamine / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / potassium ion transport / calcium-mediated signaling / response to calcium ion / sarcolemma / cellular response to type II interferon / modulation of chemical synaptic transmission / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / Z disc / spindle pole / disordered domain specific binding / calcium-dependent protein binding / protein autophosphorylation / myelin sheath / synaptic vesicle membrane / growth cone / sperm midpiece / vesicle / dendritic spine / transmembrane transporter binding / calmodulin binding / postsynaptic membrane / neuron projection / positive regulation of apoptotic process
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
Chem-1KP / 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: 1.66 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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)29,88310
Polymers29,0962
Non-polymers7888
Water2,810156
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)59,76720
Polymers58,1924
Non-polymers1,57516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15140 Å2
ΔGint-220 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.200, 66.850, 64.830
Angle α, β, γ (deg.)90.000, 93.810, 90.000
Int Tables number5
Space group name H-MC121

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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 , 5 types, 164 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
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: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2012
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.66→27.79 Å / Num. all: 38789 / Num. obs: 38789 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rsym value: 0.052 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.66-1.75.10.7331.11482228840.73399.7
1.7-1.755.20.6041.31436627730.60499.4
1.75-1.85.20.4841.61400426930.48499.4
1.8-1.865.20.3692.11355526170.36999.7
1.86-1.925.20.25931334425580.25999.5
1.92-1.985.20.1884.11285324660.18899.9
1.98-2.065.20.1395.61239823770.13999.7
2.06-2.145.20.1057.31201923040.10599.7
2.14-2.245.20.0839.21155522090.08399.7
2.24-2.355.30.06611.31103721000.06699.8
2.35-2.475.20.05712.61050820060.05799.9
2.47-2.625.30.05113.7999518990.05199.9
2.62-2.815.30.04415.1958018160.044100
2.81-3.035.30.03916.7872016590.039100
3.03-3.325.30.03516.8801215180.03599.9
3.32-3.715.20.03216.6737614080.03299.9
3.71-4.295.20.03117.8650112470.031100
4.29-5.255.20.03415.4532110240.03499.6
5.25-7.425.10.03516.941918230.03599.7
7.42-27.794.60.03915.418644080.03989.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→27.79 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8381 / SU ML: 0.17 / σ(F): 1.36 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1905 4.91 %
Rwork0.1907 --
obs0.1922 38789 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.18 Å2 / Biso mean: 40.7742 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: LAST / Resolution: 1.66→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 42 156 2139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072177
X-RAY DIFFRACTIONf_angle_d1.1612937
X-RAY DIFFRACTIONf_chiral_restr0.079324
X-RAY DIFFRACTIONf_plane_restr0.005381
X-RAY DIFFRACTIONf_dihedral_angle_d14.937855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.66-1.70150.3111560.257626152771100
1.7015-1.74750.31431320.25012619275199
1.7475-1.79890.31781260.2382627275399
1.7989-1.8570.24141230.220826222745100
1.857-1.92330.23641420.211226202762100
1.9233-2.00030.27431480.200325902738100
2.0003-2.09130.20981210.199826612782100
2.0913-2.20150.21651290.183726242753100
2.2015-2.33940.21111520.183426402792100
2.3394-2.51990.22911390.194526262765100
2.5199-2.77330.24411310.194926462777100
2.7733-3.17410.20521180.190126822800100
3.1741-3.99720.2241420.165926572799100
3.9972-27.79350.18371460.18652655280198
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)
10.01820.00460.00320.0361-0.02990.0209-0.1982-0.21550.19140.26960.0544-0.3253-0.2589-0.1802-0.00020.35090.1114-0.05580.3661-0.09820.327726.12964.762247.4856
20.01490.0054-0.00670.0013-0.00270.0029-0.0414-0.0319-0.0515-0.01560.067-0.10130.04250.16280.00070.3801-0.14830.02760.44120.07540.326144.482358.034242.5116
30.64740.0993-0.03770.39490.07010.4072-0.20160.2406-0.6041-0.0710.1155-0.2230.36920.07830.01640.2393-0.0540.02230.2872-0.0190.284259.73359.023424.0015
40.83050.10210.44670.1712-0.07380.333-0.22070.1743-0.08520.02460.0892-0.0638-0.0598-0.2104-0.04840.21470.0095-0.0140.1933-0.01120.205941.689255.992233.5308
50.43720.06290.13180.1074-0.26010.8205-0.2232-0.28210.20530.60280.11330.1095-0.5047-0.137-0.64020.79160.36950.05390.6280.0798-0.001328.845850.914959.3906
60.5802-0.1777-0.13130.7015-0.03070.0325-0.4429-0.62570.24870.70790.412-0.20450.18830.2325-0.04940.28740.1153-0.04390.3006-0.04540.184335.611445.420447.2276
70.04790.0488-0.0980.1850.24341.0415-0.00880.0572-0.1950.17420.2432-0.37920.23930.4563-0.02190.51380.2367-0.26010.4621-0.29860.349236.068954.51657.3144
81.01160.08540.23880.0558-0.03870.4147-0.05460.05440.32660.42840.226-0.42080.00640.43920.09320.3120.0809-0.07010.2762-0.07350.337223.872565.597539.396
90.4241-0.4390.22150.3673-0.18470.09980.1751-0.0463-0.3369-0.11070.10640.39480.0175-0.17050.00180.20890.0241-0.02380.2410.03490.33565.815463.199232.5149
100.0460.00060.01720.0399-0.01120.0132-0.1581-0.07970.46380.22090.085-0.3119-0.091-0.14470.00010.28140.0555-0.02950.2264-0.03130.331712.675572.102436.4353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 395 through 404 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 405 through 413 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 414 through 445 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 446 through 491 )B0
5X-RAY DIFFRACTION5chain 'R' and (resid 2 through 28 )R0
6X-RAY DIFFRACTION6chain 'R' and (resid 29 through 64 )R0
7X-RAY DIFFRACTION7chain 'R' and (resid 65 through 74 )R0
8X-RAY DIFFRACTION8chain 'R' and (resid 75 through 92 )R0
9X-RAY DIFFRACTION9chain 'R' and (resid 93 through 134 )R0
10X-RAY DIFFRACTION10chain 'R' and (resid 135 through 147 )R0

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