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Yorodumi- PDB-4ehq: Crystal Structure of Calmodulin Binding Domain of Orai1 in Comple... -
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-Basic information
Entry | Database: PDB / ID: 4ehq | ||||||
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Title | Crystal Structure of Calmodulin Binding Domain of Orai1 in Complex with Ca2+/Calmodulin Displays a Unique Binding Mode | ||||||
Components |
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Keywords | PROTEIN BINDING / calmodulin / Orai1 / calcium dependent inactivation / EF hand / Calcium binding / calcium-dependent inactivation / Calmodulin binding domain of Orai1 / none / cytosol | ||||||
Function / homology | Function and homology information store-operated calcium entry / regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / store-operated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Elevation of cytosolic Ca2+ levels ...store-operated calcium entry / regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / store-operated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / : / mammary gland epithelium development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / calcium ion import / 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 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 / protein phosphatase activator activity / plasma membrane raft / ligand-gated ion channel signaling pathway / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of calcium ion transport / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / 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 / Ion homeostasis / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / 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 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / calcium ion transmembrane transport / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel activity / positive regulation of insulin secretion / 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 / phospholipase C-activating G protein-coupled receptor signaling pathway / growth cone / basolateral plasma membrane / vesicle / transmembrane transporter binding / adaptive immune response / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of apoptotic process / membrane raft / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9005 Å | ||||||
Authors | Liu, Y. / Zheng, X. / Mueller, G.A. / Sobhany, M. / DeRose, E.F. / Zhang, Y. / London, R.E. / Birnbaumer, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal structure of calmodulin binding domain of orai1 in complex with ca2+*calmodulin displays a unique binding mode. Authors: Liu, Y. / Zheng, X. / Mueller, G.A. / Sobhany, M. / Derose, E.F. / Zhang, Y. / London, R.E. / Birnbaumer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ehq.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ehq.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ehq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/4ehq ftp://data.pdbj.org/pub/pdb/validation_reports/eh/4ehq | HTTPS FTP |
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-Related structure data
Related structure data | 1iwqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16721.350 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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#2: Protein/peptide | Mass: 2393.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96D31 | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GBL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris pH 6.0, 40% PPG P400, 14% butyrolactone, 1% n-octyl-beta-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 23, 2010 |
Radiation | Monochromator: copper anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 11939 / Num. obs: 11497 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.9 / Num. unique all: 853 / % possible all: 73.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IWQ Resolution: 1.9005→19.987 Å / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 19.33 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.125 Å2 / ksol: 0.415 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9005→19.987 Å
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Refine LS restraints |
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LS refinement shell |
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