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Yorodumi- PDB-3c16: Complex of GS-Alpha with the Catalytic Domains of Mammalian Adeny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c16 | ||||||
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Title | Complex of GS-Alpha with the Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with Adenosine-5'-Triphosphate and Ca | ||||||
Components |
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Keywords | Lyase/Lyase INHIBITOR / ADENYLYL CYCLASE / GSALPHA / cAMP biosynthesis / Glycoprotein / Lyase / Magnesium / Membrane / Metal-binding / Phosphoprotein / Transmembrane / GTP-binding / Lipoprotein / Nucleotide-binding / Palmitate / Transducer / Lyase-Lyase INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / mu-type opioid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / mu-type opioid receptor binding / regulation of insulin secretion involved in cellular response to glucose stimulus / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / beta-2 adrenergic receptor binding / cAMP-mediated signaling / adenylate cyclase binding / D1 dopamine receptor binding / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to forskolin / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase activator activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cilium / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / manganese ion binding / positive regulation of cytosolic calcium ion concentration / intracellular signal transduction / membrane raft / GTPase activity / dendrite / GTP binding / magnesium ion binding / protein-containing complex / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) Rattus norvegicus (Norway rat) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Mou, T.-C. / Sprang, S.R. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural basis for inhibition of mammalian adenylyl cyclase by calcium. Authors: Mou, T.C. / Masada, N. / Cooper, D.M. / Sprang, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c16.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c16.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/3c16 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c16 | HTTPS FTP |
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-Related structure data
Related structure data | 3c14C 3c15C 3maaC 1azsS C: citing same article (ref.) 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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Unit cell |
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-Components
-Adenylate cyclase type ... , 2 types, 2 molecules AB
#1: Protein | Mass: 25526.514 Da / Num. of mol.: 1 / Fragment: C1A DOMAIN / Mutation: V476M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: ADCY5 / Plasmid: PQE60-H6-VC1(580) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30803, adenylate cyclase |
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#2: Protein | Mass: 23717.033 Da / Num. of mol.: 1 / Fragment: C2A DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Adcy2 / Plasmid: PQE60-ARGC-IIC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26769, adenylate cyclase |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 46712.500 Da / Num. of mol.: 1 / Fragment: TRYPSINIZED FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAS, GNAS1 / Plasmid: PQE60-GSALPHA-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04896 |
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-Non-polymers , 7 types, 13 molecules
#4: Chemical | #5: Chemical | ChemComp-FOK / | #6: Chemical | ChemComp-ATP / | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-MG / | #9: Chemical | ChemComp-GSP / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.74 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 7.5-7.8% PEG 8000, 0.5M NACL, 0.1M PHOSPHATE BUFFER, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0393 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2004 Details: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0393 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→25 Å / Num. obs: 22557 / Redundancy: 2.5 % / Rmerge(I) obs: 0.176 |
Reflection shell | Resolution: 2.87→3 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 2242 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AZS Resolution: 2.87→15 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.833 / SU B: 19.97 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.9 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.663 Å2
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Refinement step | Cycle: LAST / Resolution: 2.87→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.87→2.949 Å / Total num. of bins used: 20
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