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Yorodumi- PDB-1sk6: Crystal structure of the adenylyl cyclase domain of anthrax edema... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sk6 | ||||||
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Title | Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin, 3',5' cyclic AMP (cAMP), and pyrophosphate | ||||||
Components |
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Keywords | Toxin / Lyase/Metal Binding Protein / EF3 cAMP PPi CaM / Lyase-Metal Binding 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: 3.2 Å | ||||||
Authors | Guo, Q. / Shen, Y. / Zhukovskaya, N.L. / Tang, W.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate. Authors: Guo, Q. / Shen, Y. / Zhukovskaya, N.L. / Florian, J. / Tang, W.J. | ||||||
History |
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Remark 999 | SEQUENCE Residue (B ASN 521 ) and Residue (B GLU 524 ) are linked together. Residue (C PHE 773 ) ...SEQUENCE Residue (B ASN 521 ) and Residue (B GLU 524 ) are linked together. Residue (C PHE 773 ) and Residue (C LYS 774 ) are not linked, distance of C-N bond is 1.80. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sk6.cif.gz | 372.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sk6.ent.gz | 298.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sk6_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1sk6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1sk6_validation.xml.gz | 83.7 KB | Display | |
Data in CIF | 1sk6_validation.cif.gz | 111.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/1sk6 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/1sk6 | 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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-Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 58810.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: CYA, PXO1-122 / Plasmid: ProEx-H6-EF3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 pUBS520 / References: UniProt: P40136, adenylate cyclase #2: Protein | Mass: 16721.350 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02593, UniProt: P0DP23*PLUS |
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-Non-polymers , 4 types, 21 molecules
#3: Chemical | ChemComp-YB / #4: Chemical | #5: Chemical | #6: 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: 3.95 Å3/Da / Density % sol: 68.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2003 |
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: 3.2→50 Å / Num. all: 50041 / Num. obs: 48122 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.13 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6739 / Rsym value: 0.484 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1k90 Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 3.2 Å / Rfactor Rfree error: 0.005
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