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Yorodumi- PDB-2mgu: Structure of the complex between calmodulin and the binding domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mgu | ||||||
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Title | Structure of the complex between calmodulin and the binding domain of HIV-1 matrix protein | ||||||
Components |
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Keywords | PROTEIN BINDING / calmodulin / HIV-1 matrix | ||||||
Function / homology | Function and homology information 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 / viral budding via host ESCRT complex / 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 / response to calcium ion / Schaffer collateral - CA1 synapse / ISG15 antiviral mechanism / cellular response to type II interferon / host multivesicular body / G2/M transition of mitotic cell cycle / spindle pole / calcium-dependent protein binding / disordered domain specific binding / myelin sheath / growth cone / viral nucleocapsid / protein autophosphorylation / vesicle / transmembrane transporter binding / host cell cytoplasm / neuron projection / protein domain specific binding / positive regulation of apoptotic process / centrosome / calcium ion binding / host cell nucleus / protein kinase binding / host cell plasma membrane / structural molecule activity / virion membrane / protein-containing complex / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Vlach, J. / Samal, A. / Saad, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Solution Structure of Calmodulin Bound to the Binding Domain of the HIV-1 Matrix Protein. Authors: Vlach, J. / Samal, A.B. / Saad, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mgu.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mgu.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2mgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mgu_validation.pdf.gz | 417.6 KB | Display | wwPDB validaton report |
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Full document | 2mgu_full_validation.pdf.gz | 665.7 KB | Display | |
Data in XML | 2mgu_validation.xml.gz | 74.8 KB | Display | |
Data in CIF | 2mgu_validation.cif.gz | 90.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/2mgu ftp://data.pdbj.org/pub/pdb/validation_reports/mg/2mgu | 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.) 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: 4317.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: Q7ZJG2, UniProt: P12493*PLUS |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.1-1.2 mM [U-95% 13C; U-95% 15N] calmodulin, 0.1-1.2 mM MA8-43, 5 mM CALCIUM ION, 100% D2O Solvent system: 100% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.015 / pH: 6.3 / Pressure: ambient / Temperature: 308 K |
-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: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |