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- PDB-4g27: Calcium-calmodulin complexed with the calmodulin binding domain f... -

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Basic information

Entry
Database: PDB / ID: 4g27
TitleCalcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant and phenylurea
Components
  • Calmodulin
  • Small conductance calcium-activated potassium channel protein 2
KeywordsMETAL TRANSPORT/CALCIUM BINDING PROTEIN / protein-protein complex / EF Hand / metal binding protein / METAL TRANSPORT-CALCIUM BINDING PROTEIN 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 / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / 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 / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / alpha-actinin binding / protein phosphatase activator activity / smooth endoplasmic reticulum / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase 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 / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / 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 / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / 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 / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / postsynaptic membrane / vesicle / transmembrane transporter binding / dendritic spine / protein autophosphorylation / 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
1-phenylurea / 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: 1.65 Å
AuthorsZhang, M. / Pascal, J.M. / Zhang, J.-F.
CitationJournal: Nat Commun / Year: 2012
Title: Identification of the functional binding pocket for compounds targeting small-conductance Ca(2+)-activated potassium channels.
Authors: Zhang, M. / Pascal, J.M. / Schumann, M. / Armen, R.S. / Zhang, J.F.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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_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)29,6939
Polymers29,0962
Non-polymers5977
Water3,747208
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)59,38518
Polymers58,1924
Non-polymers1,19314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14300 Å2
ΔGint-194 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 66.870, 65.130
Angle α, β, γ (deg.)90.00, 93.31, 90.00
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 / small conductance potassium channel splice variant / 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, 215 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PHU / 1-phenylurea / Phenylurea


Mass: 136.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
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 298K

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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: 1.65→50 Å / Num. all: 39245 / Num. obs: 39245 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 22.5
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2902 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDS(xia2)data reduction
XDS(xia2data scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→39.072 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1934 4.93 %RANDOM
Rwork0.191 ---
obs0.1928 39243 99.41 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.693 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8603 Å20 Å2-5.7342 Å2
2--1.6059 Å20 Å2
3----0.7455 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 33 208 2100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111926
X-RAY DIFFRACTIONf_angle_d1.2642583
X-RAY DIFFRACTIONf_dihedral_angle_d13.243753
X-RAY DIFFRACTIONf_chiral_restr0.072288
X-RAY DIFFRACTIONf_plane_restr0.006345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.34091640.2942640X-RAY DIFFRACTION100
1.6913-1.7370.36051250.27462639X-RAY DIFFRACTION100
1.737-1.78810.25561340.25562664X-RAY DIFFRACTION100
1.7881-1.84580.281250.2442666X-RAY DIFFRACTION100
1.8458-1.91180.27311400.22182698X-RAY DIFFRACTION100
1.9118-1.98830.26761540.21322622X-RAY DIFFRACTION99
1.9883-2.07880.23521330.19152663X-RAY DIFFRACTION100
2.0788-2.18840.2111260.17692698X-RAY DIFFRACTION100
2.1884-2.32550.23661560.18262655X-RAY DIFFRACTION100
2.3255-2.50510.2211480.18022643X-RAY DIFFRACTION100
2.5051-2.75710.22761280.18022693X-RAY DIFFRACTION100
2.7571-3.15590.2181200.18362714X-RAY DIFFRACTION100
3.1559-3.97550.23821390.16962697X-RAY DIFFRACTION100
3.9755-39.08250.19351420.19452617X-RAY DIFFRACTION95
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)
19.2885-7.2302-2.24959.58821.07734.4799-0.4134-0.65530.90730.24590.3426-0.7797-0.04880.1976-0.03580.32960.0859-0.07320.3232-0.07080.276729.663462.619547.0078
24.74510.2647-2.37235.1072-1.64019.0622-0.04130.3745-0.4178-0.17240.0519-0.23420.02480.16830.0360.0909-0.0407-0.03450.1812-0.07050.188859.629159.680423.551
36.13860.9327-5.82910.7294-0.99098.269-0.09190.1545-0.01740.02650.0814-0.073-0.2232-0.18320.00220.14120.009-0.05840.1214-0.02920.176442.267456.373432.9658
41.29760.0080.68790.9259-0.99933.3164-0.3141-0.32110.21430.62470.12720.0533-0.643-0.1417-0.22580.73080.32540.02650.53240.08840.153528.784851.020159.7508
51.8115-0.59882.24510.6237-0.65765.1381-0.5873-0.58780.27170.74130.3451-0.1489-0.03550.19710.12560.32460.1407-0.05880.2598-0.03270.213635.644545.558447.4007
63.5772-2.06883.86332.2783-2.20294.2325-0.17730.2780.26880.2139-0.067-0.3282-0.06220.49920.21760.52870.3038-0.28620.6134-0.24040.464836.093555.420857.3047
78.16080.06947.24353.77610.07158.1725-0.57080.34490.6890.25920.191-0.3184-0.56630.74460.35510.1810.0367-0.00490.2094-0.01540.248822.426466.551937.3537
83.7714-0.6350.86339.0661-3.26542.870.16330.1851-0.606-0.55080.1470.3170.4237-0.2571-0.24160.19520.0239-0.05640.2145-0.02720.26058.599160.971429.7771
93.8356-0.92081.17182.0969-2.73474.1577-0.0473-0.4309-0.59880.26240.52410.7569-0.0898-0.4158-0.36320.17890.05970.0130.29120.06780.32632.325366.963137.0463
107.587-0.44434.81146.8465-0.5253.4856-0.5237-0.28220.88110.50060.0975-0.4456-0.8445-0.32480.35850.24530.051-0.04150.1649-0.02410.289912.992872.327436.3225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 395:414)
2X-RAY DIFFRACTION2chain 'B' and (resseq 415:445)
3X-RAY DIFFRACTION3chain 'B' and (resseq 446:489)
4X-RAY DIFFRACTION4chain 'R' and (resseq 2:28)
5X-RAY DIFFRACTION5chain 'R' and (resseq 29:64)
6X-RAY DIFFRACTION6chain 'R' and (resseq 65:75)
7X-RAY DIFFRACTION7chain 'R' and (resseq 76:92)
8X-RAY DIFFRACTION8chain 'R' and (resseq 93:117)
9X-RAY DIFFRACTION9chain 'R' and (resseq 118:134)
10X-RAY DIFFRACTION10chain 'R' and (resseq 135:147)

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