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- PDB-1ne4: Crystal Structure of Rp-cAMP Binding R1a Subunit of cAMP-dependen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ne4 | ||||||
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Title | Crystal Structure of Rp-cAMP Binding R1a Subunit of cAMP-dependent Protein Kinase | ||||||
![]() | cAMP-dependent protein kinase type I-alpha regulatory chain | ||||||
![]() | HYDROLASE / cAMP-dependent protein kinase / R1a subunit / cAMP analog / Rp-cAMP | ||||||
Function / homology | ![]() : / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity ...: / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / cAMP-dependent protein kinase inhibitor activity / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / sarcomere organization / cellular response to glucagon stimulus / negative regulation of activated T cell proliferation / plasma membrane raft / protein kinase A catalytic subunit binding / axoneme / immunological synapse / mesoderm formation / cAMP binding / multivesicular body / regulation of protein phosphorylation / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / protein domain specific binding / negative regulation of gene expression / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, J. / Jones, J.M. / Xuong, N.H. / Taylor, S.S. | ||||||
![]() | ![]() Title: Crystal Structures of RIalpha Subunit of Cyclic Adenosine 5'-Monophosphate (cAMP)-Dependent Protein Kinase Complexed with (R(p))-Adenosine 3',5'-Cyclic Monophosphothioate and (S(p))-Adenosine ...Title: Crystal Structures of RIalpha Subunit of Cyclic Adenosine 5'-Monophosphate (cAMP)-Dependent Protein Kinase Complexed with (R(p))-Adenosine 3',5'-Cyclic Monophosphothioate and (S(p))-Adenosine 3',5'-Cyclic Monophosphothioate, the Phosphothioate Analogues of cAMP. Authors: Wu, J. / Jones, J.M. / Xuong, N.H. / Eyck, L.F. / Taylor, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ne6C ![]() 1rgsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31880.104 Da / Num. of mol.: 1 / Fragment: 1-91 deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.27 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: amino sulfate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.5K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 5, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 16306 / Num. obs: 15769 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.046 / Net I/σ(I): 47.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 6.3 / Num. unique all: 1566 / Rsym value: 0.473 / % possible all: 97.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 16251 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 97.9 % / Rmerge(I) obs: 0.473 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RGS Resolution: 2.4→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 55.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.051
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |