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Yorodumi- PDB-1lvc: Crystal structure of the adenylyl cyclase domain of anthrax edema... -
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-Basic information
Entry | Database: PDB / ID: 1lvc | ||||||
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Title | Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP | ||||||
Components |
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Keywords | LYASE / helical domain / protein-protein complex | ||||||
Function / homology | Function and homology information regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / adenylate cyclase ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / calcium- and calmodulin-responsive adenylate cyclase activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / adenylate cyclase / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / cAMP biosynthetic process / establishment of protein localization to membrane / adenylate cyclase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / 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 / host cell cytosol / 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 / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / 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 / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel 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 / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / small molecule binding / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 Å | ||||||
Authors | Shen, Y. / Lee, Y.-S. / Soelaiman, S. / Bergson, P. / Lu, D. / Chen, A. / Beckingham, K. / Grabarek, Z. / Mrksich, M. / Tang, W.-J. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins Authors: Shen, Y. / Lee, Y.-S. / Soelaiman, S. / Bergson, P. / Lu, D. / Chen, A. / Beckingham, K. / Grabarek, Z. / Mrksich, M. / Tang, W.-J. #1: Journal: Nature / Year: 2002 Title: Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin Authors: Drum, C.L. / Yan, S.Z. / Bard, J. / Shen, Y.Q. / Lu, D. / Soelaiman, S. / Grabarek, Z. / Bohm, A. / Tang, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lvc.cif.gz | 389 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lvc.ent.gz | 313.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lvc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1lvc_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1lvc_validation.xml.gz | 87.7 KB | Display | |
Data in CIF | 1lvc_validation.cif.gz | 114 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvc ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvc | HTTPS FTP |
-Related structure data
Related structure data | 1k90S 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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2 |
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3 |
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Unit cell |
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Details | The biological assembly is monomer |
-Components
#1: Protein | Mass: 58810.605 Da / Num. of mol.: 3 / Fragment: c-terminal domain (residues 291-800) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Plasmid: pProEx / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P40136, adenylate cyclase #2: Protein | Mass: 16852.545 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02593, UniProt: P0DP23*PLUS #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknownDetails: Hiratsuka, T., (1983) Biochem. Biophys. Acta., 742, 496. |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→29.96 Å / Num. all: 39156 / Num. obs: 38841 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 10 / Num. unique all: 3871 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 3.6 Å / Redundancy: 6.85 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1K90 Resolution: 3.6→29.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 457541.92 / Data cutoff high rms absF: 457541.92 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.5231 Å2 / ksol: 0.25238 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.83 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.6 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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