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- PDB-1qx7: Crystal structure of apoCaM bound to the gating domain of small c... -

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Basic information

Entry
Database: PDB / ID: 1qx7
TitleCrystal structure of apoCaM bound to the gating domain of small conductance Ca2+-activated potassium channel
Components
  • Calmodulin
  • Small conductance calcium-activated potassium channel protein 2
KeywordsSIGNALING PROTEIN / apoCalmodulin / SK channel / small conductance Ca2+ activated K+ channel / CaMBD / gating domain / Ca2+-activated gating / functioanl bipartism
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 / Potassium channel domain / Ion channel / EF-hand / Recoverin; domain 1 ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / 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 / 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 combined with MAD / Resolution: 3.09 Å
AuthorsSchumacher, M.A. / Crum, M. / Miller, M.C.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
Authors: Schumacher, M.A. / Crum, M. / Miller, M.C.
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Calmodulin
R: Calmodulin
A: Calmodulin
B: Calmodulin
M: Calmodulin
D: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)95,9346
Polymers95,9346
Non-polymers00
Water0
1
I: Calmodulin
R: Calmodulin


Theoretical massNumber of molelcules
Total (without water)34,2872
Polymers34,2872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-41 kcal/mol
Surface area14440 Å2
MethodPISA
2
A: Calmodulin
B: Calmodulin


Theoretical massNumber of molelcules
Total (without water)34,2872
Polymers34,2872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area14100 Å2
MethodPISA
3
M: Calmodulin
D: Small conductance calcium-activated potassium channel protein 2


Theoretical massNumber of molelcules
Total (without water)27,3602
Polymers27,3602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Calmodulin

A: Calmodulin
B: Calmodulin


Theoretical massNumber of molelcules
Total (without water)51,4303
Polymers51,4303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-46 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.930, 79.930, 220.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe apoCaM/CaMBD complex is monomeric, also in the crystal are two domain swapped dimers of apoCaM which "anchor" the flexible apoCaM/CaMBD complex

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Components

#1: Protein
Calmodulin /


Mass: 17143.406 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: CALM1, CAM1, CALM, CAM, CALM2, CAM2, CAMB, CALM3, CAM3, CAMC
Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein Small conductance calcium-activated potassium channel protein 2 / SK2


Mass: 10216.989 Da / Num. of mol.: 1 / Fragment: SK2 gating domain (residues 411-487)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: KCNN2 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P70604

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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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Citrate, NaCl, Hepes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.09→75.16 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.09→3.51 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: molecular replacement combined with MAD
Starting model: 1QX5

1qx5


Resolution: 3.09→75.16 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3330198.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1958 9.5 %RANDOM
Rwork0.286 ---
obs0.286 22535 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.9875 Å2 / ksol: 0.365198 e/Å3
Displacement parametersBiso mean: 69.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.11 Å20 Å20 Å2
2--9.11 Å20 Å2
3----18.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.09→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5523 0 0 0 5523
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.09→3.51 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 324 9.4 %
Rwork0.35 3416 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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