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Open data
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Basic information
Entry | Database: PDB / ID: 1qx5 | ||||||
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Title | Crystal structure of apoCalmodulin | ||||||
![]() | Calmodulin | ||||||
![]() | SIGNALING PROTEIN / apoCalmodulin / domain swap / dimer / EF hands / calcium binding protein | ||||||
Function / homology | ![]() regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / presynaptic cytosol / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / : / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / calcium channel inhibitor activity / phosphatidylinositol 3-kinase binding / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / titin binding / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / spindle microtubule / calcium-mediated signaling / positive regulation of receptor signaling pathway via JAK-STAT / Schaffer collateral - CA1 synapse / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schumacher, M.A. / Crum, M. / Miller, M.C. | ||||||
![]() | ![]() Title: Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex. Authors: Schumacher, M.A. / Crum, M. / Miller, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.4 KB | Display | ![]() |
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PDB format | ![]() | 191.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | apoCaM forms a domain swapped dimer: there are four, essentially identical dimers in the ASU |
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Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CALM1, CAM1, CALM, CAM, CALM2, CAM2, CAMB, CALM3, CAM3, CAMC Plasmid: pET23b / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Citrate, 150 mM NaCl, Hepes , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→66.4 Å / Num. all: 61810 / Num. obs: 61810 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.047 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.54→2.7 Å / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.8149 Å2 / ksol: 0.374381 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.48 Å / Luzzati sigma a free: 0.51 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→66.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.54→2.7 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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