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Yorodumi- PDB-2m55: NMR structure of the complex of an N-terminally acetylated alpha-... -
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-Basic information
Entry | Database: PDB / ID: 2m55 | ||||||
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Title | NMR structure of the complex of an N-terminally acetylated alpha-synuclein peptide with calmodulin | ||||||
Components |
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Keywords | CALCIUM BINDING PROTEIN/PROTEIN FIBRIL / Protein/peptide / Ca-binding / CALCIUM BINDING PROTEIN-PROTEIN FIBRIL complex | ||||||
Function / homology | Function and homology information : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / CaM pathway / regulation of norepinephrine uptake / Cam-PDE 1 activation / Sodium/Calcium exchangers / SNARE complex assembly / positive regulation of neurotransmitter secretion / Calmodulin induced events / regulation of synaptic vesicle endocytosis / dopamine biosynthetic process / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / synaptic vesicle priming / regulation of macrophage activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / negative regulation of microtubule polymerization / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / synaptic vesicle transport / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / dopamine uptake involved in synaptic transmission / positive regulation of DNA binding / dynein complex binding / regulation of dopamine secretion / positive regulation of receptor recycling / positive regulation of ryanodine-sensitive calcium-release channel activity / protein kinase inhibitor activity / nitric-oxide synthase binding / 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 / negative regulation of thrombin-activated receptor signaling pathway / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / response to type II interferon / cuprous ion binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / positive regulation of exocytosis / RHO GTPases activate PAKs / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / : / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / response to magnesium ion / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / synaptic vesicle endocytosis / regulation of presynapse assembly / catalytic complex / DARPP-32 events / negative regulation of serotonin uptake / detection of calcium ion / regulation of cardiac muscle contraction / alpha-tubulin binding / regulation of ryanodine-sensitive calcium-release channel activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Gruschus, J.M. / Yap, T. / Pistolesi, S. / Maltsev, A.S. / Lee, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: NMR Structure of Calmodulin Complexed to an N-Terminally Acetylated alpha-Synuclein Peptide. Authors: Gruschus, J.M. / Yap, T.L. / Pistolesi, S. / Maltsev, A.S. / Lee, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m55.cif.gz | 1000.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m55.ent.gz | 847.8 KB | Display | PDB format |
PDBx/mmJSON format | 2m55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m55_validation.pdf.gz | 552.1 KB | Display | wwPDB validaton report |
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Full document | 2m55_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 2m55_validation.xml.gz | 438.3 KB | Display | |
Data in CIF | 2m55_validation.cif.gz | 333.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/2m55 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/2m55 | 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) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Plasmid: pet30b / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS |
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#2: Protein/peptide | Mass: 1979.410 Da / Num. of mol.: 1 / Fragment: UNP residues 1-19 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P37840 |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.36 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | |||||||||
NMR constraints | NOE constraints total: 3467 / Protein phi angle constraints total count: 140 / Protein psi angle constraints total count: 140 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |