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Yorodumi- PDB-3maa: Complex of GS-Alpha with the Catalytic Domains of Mammalian Adeny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3maa | |||||||||
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Title | Complex of GS-Alpha with the Catalytic Domains of Mammalian Adenylyl Cyclase: Complex with Adenosine 5-O-(l-Thiophosphate) and Low Ca Concentration | |||||||||
Components |
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Keywords | LYASE/LYASE INHIBITOR / ADENYLYL CYCLASE / G(S)ALPHA / ATP-ALPHA-S / CALCIUM ION / 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 / regulation of insulin secretion involved in cellular response to glucose stimulus / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity ...Adenylate cyclase activating pathway / Hedgehog 'off' state / PKA activation / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / cAMP biosynthetic process / G alpha (z) signalling events / adenylate cyclase activity / adenylate cyclase binding / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to forskolin / adenylate cyclase activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cAMP-mediated signaling / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cilium / 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: 3 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 | 3maa.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3maa.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 3maa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3maa_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3maa_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3maa_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 3maa_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/3maa ftp://data.pdbj.org/pub/pdb/validation_reports/ma/3maa | HTTPS FTP |
-Related structure data
Related structure data | 3c14C 3c15C 3c16C 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, ADENYLYL CYCLASE TYPE V / Plasmid: PQE60-H6-VC1(580) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / 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, ADENYLYL CYCLASE TYPE II / Plasmid: PQE60-ARGC-IIC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P26769, adenylate cyclase |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 45769.527 Da / Num. of mol.: 1 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): BL-21 / References: UniProt: P04896 |
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-Non-polymers , 7 types, 18 molecules
#4: Chemical | ChemComp-FKP / |
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#5: Chemical | ChemComp-CA / |
#6: Chemical | ChemComp-TAT / |
#7: Chemical | ChemComp-MG / |
#8: Chemical | ChemComp-GSP / |
#9: Chemical | ChemComp-CL / |
#10: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 5.6 Details: 7.5-7.8% PEG8000, 0.5M NACL, 0.1M PHOSPHATE BUFFER, pH 5.6, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.0231 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2008 Details: VERTICAL FOCUSING MIRROR, SINGLE CRYSTAL Si(311) BENT MONOCHROMATOR |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0231 Å / Relative weight: 1 |
Reflection | Resolution: 3→25 Å / Num. obs: 20034 / % possible obs: 82.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.84 Å2 / Rsym value: 0.175 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 3→3.077 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.0305 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1606 / Rsym value: 0.414 / % possible all: 2.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AZS Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.776 / SU B: 25.196 / SU ML: 0.454 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.811 / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 31.84 Å2
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Refinement step | Cycle: LAST / Resolution: 3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
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