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- PDB-1g4y: 1.60 A CRYSTAL STRUCTURE OF THE GATING DOMAIN FROM SMALL CONDUCTA... -

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Basic information

Entry
Database: PDB / ID: 1g4y
Title1.60 A CRYSTAL STRUCTURE OF THE GATING DOMAIN FROM SMALL CONDUCTANCE POTASSIUM CHANNEL COMPLEXED WITH CALCIUM-CALMODULIN
Components
  • CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2
  • CALMODULIN
KeywordsSIGNALING PROTEIN / small-conductance calcium-activated potassium channel / calmodulin / calmodulin binding domain (CaMBD) / channel gating
Function / homology
Function and homology information


Ca2+ activated K+ channels / regulation of store-operated calcium channel activity / small conductance calcium-activated potassium channel activity / : / regulation of high voltage-gated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / 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 / : / regulation of high voltage-gated calcium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transport / inward rectifier potassium channel activity / 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 / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / smooth endoplasmic reticulum / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / T-tubule / sperm midpiece / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / modulation of chemical synaptic transmission / calcium-mediated signaling / potassium ion transport / sarcolemma / Schaffer collateral - CA1 synapse / cellular response to type II interferon / Z disc / response to calcium ion / spindle pole / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / protein autophosphorylation / vesicle / dendritic spine / transmembrane transporter binding / postsynaptic membrane / calmodulin binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / centrosome / calcium ion binding / protein kinase binding / glutamatergic synapse / cell surface / protein homodimerization activity
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 ...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 / : / Recoverin; domain 1 / 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 / MIR / Resolution: 1.6 Å
AuthorsSchumacher, M.A. / Rivard, A. / Bachinger, H.P. / Adelman, J.P.
CitationJournal: Nature / Year: 2001
Title: Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin.
Authors: Schumacher, M.A. / Rivard, A.F. / Bachinger, H.P. / Adelman, J.P.
History
DepositionJan 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 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_asym_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.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2
R: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0035
Polymers28,8272
Non-polymers1763
Water3,585199
1
B: CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2
R: CALMODULIN
hetero molecules

B: CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2
R: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,00610
Polymers57,6534
Non-polymers3526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12340 Å2
ΔGint-127 kcal/mol
Surface area23100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.650, 66.690, 64.690
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-806-

HOH

21B-818-

HOH

Detailsthe relevant dimer is generated by crystallographic symmetry.

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Components

#1: Protein CALCIUM-ACTIVATED POTASSIUM CHANNEL RSK2


Mass: 12105.248 Da / Num. of mol.: 1 / Fragment: CALMODULIN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RAT / Plasmid: PET23B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604
#2: Protein CALMODULIN


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RAT / Plasmid: PET33B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulphate, lithium sulphate, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
250 mM1dropNaCl
310 mM1dropCaCl2
41.25 M1reservoirLi2SO4
50.5 Mammonium sulfate1reservoir
60.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2000 / Details: mirrors
RadiationMonochromator: double-crystal Si 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 115320 / Num. obs: 40694 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 5 / Net I/σ(I): 8.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5200 / Rsym value: 28.9 / % possible all: 87.9
Reflection
*PLUS
Num. measured all: 115320

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Processing

Software
NameVersionClassification
PHASESphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR
Starting model: room temp model

Resolution: 1.6→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh and huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4091 -random
Rwork0.221 ---
all0.212 43485 --
obs0.212 40687 93.6 %-
Displacement parametersBiso mean: 4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.023 Å0.02 Å
Luzzati d res low-6 Å
Luzzati sigma a0.262 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 7 199 2044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.57
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 4 Å2

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