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Yorodumi- PDB-2kne: Calmodulin wraps around its binding domain in the plasma membrane... -
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-Basic information
Entry | Database: PDB / ID: 2kne | ||||||
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Title | Calmodulin wraps around its binding domain in the plasma membrane CA2+ pump anchored by a novel 18-1 motif | ||||||
Components |
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Keywords | METAL TRANSPORT / protein/peptide / calcium pump / calmodulin / Acetylation / Calcium / Isopeptide bond / Methylation / Phosphoprotein / Polymorphism / Ubl conjugation / ATP-binding / Hydrolase / Membrane / Nucleotide-binding / Transmembrane | ||||||
Function / homology | Function and homology information negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / : / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / nitric-oxide synthase inhibitor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process ...negative regulation of the force of heart contraction / negative regulation of arginine catabolic process / negative regulation of cellular response to vascular endothelial growth factor stimulus / negative regulation of citrulline biosynthetic process / calcium ion transmembrane transporter activity / : / cellular response to acetylcholine / negative regulation of nitric oxide mediated signal transduction / nitric-oxide synthase inhibitor activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of peptidyl-cysteine S-nitrosylation / negative regulation of nitric-oxide synthase activity / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / sperm principal piece / calcium ion export / response to hydrostatic pressure / regulation of sodium ion transmembrane transport / flagellated sperm motility / P-type Ca2+ transporter / neural retina development / : / regulation of cell cycle G1/S phase transition / urinary bladder smooth muscle contraction / P-type calcium transporter activity / negative regulation of nitric oxide biosynthetic process / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / ATPase-coupled monoatomic cation transmembrane transporter activity / protein phosphatase 2B binding / positive regulation of cAMP-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / calcium ion transmembrane import into cytosol / regulation of synaptic vesicle endocytosis / negative regulation of cardiac muscle hypertrophy in response to stress / Calmodulin induced events / Reduction of cytosolic Ca++ levels / negative regulation of calcineurin-NFAT signaling cascade / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / plasma membrane => GO:0005886 / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / negative regulation of blood vessel endothelial cell migration / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / transport across blood-brain barrier / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / calcium ion import across plasma membrane / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac conduction / Smooth Muscle Contraction / sperm flagellum / sodium channel regulator activity / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / presynaptic active zone membrane / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Juranic, N. / Atanasova, E. / Filoteo, A.G. / Macura, S. / Prendergast, F.G. / Penniston, J.T. / Strehler, E.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Calmodulin wraps around its binding domain in the plasma membrane Ca2+ pump anchored by a novel 18-1 motif. Authors: Juranic, N. / Atanasova, E. / Filoteo, A.G. / Macura, S. / Prendergast, F.G. / Penniston, J.T. / Strehler, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kne.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2kne.ent.gz | 911 KB | Display | PDB format |
PDBx/mmJSON format | 2kne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kne_validation.pdf.gz | 555.3 KB | Display | wwPDB validaton report |
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Full document | 2kne_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2kne_validation.xml.gz | 207.8 KB | Display | |
Data in CIF | 2kne_validation.cif.gz | 168.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/2kne ftp://data.pdbj.org/pub/pdb/validation_reports/kn/2kne | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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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.) Homo sapiens (human) / Strain: BL21(DE3)-pLysS Gene: CALM, CALM1, CALM2, CALM3, CALML2, CAM, CAM1, CAM2, CAM3, CAMB, CAMC, CAMIII Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62158, UniProt: P0DP23*PLUS |
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#2: Protein/peptide | Mass: 3359.993 Da / Num. of mol.: 1 / Fragment: UNP residues 1086-1113, C28 Source method: isolated from a genetically manipulated source Details: calmodulin binding domain of PMCA C-tail / Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: ATP2B4, hCG_18445, RP11-397P13.1-001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: B1APW6, UniProt: P23634*PLUS |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Structure of holo-calmodulin in complex with C28 peptide from C-tail calmodulin-binding-domain of plasma-membrane-calcium-pump | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: REFINEMENT ALSO USES THE PROTEIN (CALMODULIN) & PEPTIDE (C28) RESIDUAL DIPOLAR COUPLINGS (BACKBONE NH, NCO and COCA) MEASURED IN A PHAGE-FILAMENTS ORIENTED MEDIA. | ||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 2446 / NOE intraresidue total count: 1113 / NOE long range total count: 315 / NOE medium range total count: 355 / NOE sequential total count: 664 / Protein other angle constraints total count: 136 / Protein phi angle constraints total count: 154 / Protein psi angle constraints total count: 150 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: -0.7 Å / Maximum torsion angle constraint violation: 10 ° / Maximum upper distance constraint violation: 0.6 Å / Torsion angle constraint violation method: XPLOR-NIH | ||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.055 Å / Distance rms dev error: 0.005 Å |