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- PDB-4g28: Calcium-calmodulin complexed with the calmodulin binding domain f... -

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Basic information

Entry
Database: PDB / ID: 4g28
TitleCalcium-calmodulin complexed with the calmodulin binding domain from a small conductance potassium channel splice variant and EBIO-1
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 / 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 / regulation of cell communication by electrical coupling involved in cardiac conduction / nitric-oxide synthase binding / adenylate cyclase binding / protein phosphatase activator activity / regulation of synaptic vesicle endocytosis / monoatomic ion channel activity / regulation of neuronal synaptic plasticity / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / phosphatidylinositol 3-kinase binding / positive regulation of nitric-oxide synthase activity / activation of adenylate cyclase activity / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / enzyme regulator activity / 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 / regulation of cytokinesis / response to amphetamine / protein serine/threonine kinase activator activity / spindle microtubule / sarcomere / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel regulator activity / potassium ion transport / calcium-mediated signaling / sarcolemma / response to calcium ion / 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
1-ethyl-1,3-dihydro-2H-benzimidazol-2-one / 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: 1.63 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_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)29,7199
Polymers29,0962
Non-polymers6237
Water4,504250
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)59,43718
Polymers58,1924
Non-polymers1,24514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14230 Å2
ΔGint-195 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.020, 66.670, 64.920
Angle α, β, γ (deg.)90.00, 94.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-621-

HOH

21R-1216-

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 / 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, 257 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: Chemical ChemComp-0W8 / 1-ethyl-1,3-dihydro-2H-benzimidazol-2-one


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 56.95 %
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: 1.63→25 Å / Num. all: 40567 / Num. obs: 40567 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.3
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 5 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2989 / % possible all: 99.5

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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: 1.63→22.92 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1998 4.93 %RANDOM
Rwork0.1918 ---
obs0.1935 40565 99.14 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.24 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9075 Å20 Å2-4.0202 Å2
2--5.6611 Å20 Å2
3----3.7536 Å2
Refinement stepCycle: LAST / Resolution: 1.63→22.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1859 0 35 250 2144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111929
X-RAY DIFFRACTIONf_angle_d1.2582589
X-RAY DIFFRACTIONf_dihedral_angle_d13.096756
X-RAY DIFFRACTIONf_chiral_restr0.073288
X-RAY DIFFRACTIONf_plane_restr0.006351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.67080.30361690.26492717X-RAY DIFFRACTION100
1.6708-1.71590.31191420.26092743X-RAY DIFFRACTION100
1.7159-1.76640.29481360.25592782X-RAY DIFFRACTION99
1.7664-1.82340.2891510.24992745X-RAY DIFFRACTION100
1.8234-1.88850.26681150.22722759X-RAY DIFFRACTION100
1.8885-1.96410.25061740.21062764X-RAY DIFFRACTION99
1.9641-2.05340.25441470.20092708X-RAY DIFFRACTION100
2.0534-2.16160.20471080.18852801X-RAY DIFFRACTION99
2.1616-2.29690.23491530.18692746X-RAY DIFFRACTION99
2.2969-2.47410.22711530.18342734X-RAY DIFFRACTION99
2.4741-2.72270.22431440.18572744X-RAY DIFFRACTION99
2.7227-3.11590.21041140.1872813X-RAY DIFFRACTION99
3.1159-3.92250.2231490.16952797X-RAY DIFFRACTION100
3.9225-22.92240.1981430.18592714X-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)
14.5806-5.6388-1.34097.7270.6293.0377-0.176-0.3930.89340.13220.2927-0.95610.06190.2973-0.14110.24860.0904-0.05070.2425-0.08470.274729.345362.641446.8241
25.01280.4243-1.87474.8281-1.28637.6576-0.08980.3378-0.3289-0.08290.1378-0.23040.0220.15530.0230.1029-0.0571-0.02210.1361-0.05970.18659.629959.588923.5799
37.16240.701-6.83330.6948-0.6868.5731-0.13920.08350.0040.02430.1059-0.0779-0.0837-0.06740.03990.121-0.0001-0.04320.094-0.02010.150342.140356.367132.8949
40.71730.13930.41460.5911-0.53972.9982-0.1675-0.18660.13250.32220.09780.0473-0.4289-0.1088-0.15420.60990.31380.0330.45130.06870.091728.457450.975559.4654
51.8062-0.81641.77140.7714-1.15956.0943-0.5604-0.55260.29910.66570.3128-0.2052-0.08170.25730.17050.29050.1267-0.05290.2168-0.04090.214735.385845.554947.2248
63.311-3.78453.38064.5845-3.50493.9556-0.08880.15330.34510.1141-0.2138-0.4998-0.15470.22530.30550.53740.2974-0.25160.4739-0.19470.411935.890455.537556.9126
77.65230.56476.71632.77460.70756.0855-0.38770.27450.56840.11210.1546-0.2299-0.43230.53060.30820.17470.042200.1521-0.00720.232222.110666.513837.0778
82.1008-0.79270.92535.5433-1.77751.67120.1449-0.0641-0.5727-0.17860.17790.55840.1948-0.207-0.28580.1270.0158-0.05790.16260.0310.2995.727963.354832.3869
97.8213-1.86575.22514.9618-2.10383.9087-0.4595-0.23890.75680.42180.1141-0.4446-0.8362-0.16540.35580.22750.0413-0.00750.1381-0.02470.271212.734772.281636.1065
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 93:134)
9X-RAY DIFFRACTION9chain 'R' and (resseq 135:147)

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