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- PDB-1b9x: STRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION-REGULATE... -
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Basic information
Entry | Database: PDB / ID: 1b9x | ||||||
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Title | STRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION-REGULATED INTERACTION WITH TRANSDUCIN | ||||||
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![]() | SIGNALING PROTEIN / PHOSDUCIN / TRANSDUCIN / BETA-GAMMA / SIGNAL TRANSDUCTION / REGULATION / PHOSPHORYLATION / G PROTEINS / THIOREDOXIN / VISION / MEKA / COMPLEX (TRANSDUCER- TRANSDUCTION) | ||||||
Function / homology | ![]() Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / photoreceptor outer segment / visual perception / photoreceptor inner segment / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / G protein-coupled receptor signaling pathway / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaudet, R. / Sigler, P.B. | ||||||
![]() | ![]() Title: A molecular mechanism for the phosphorylation-dependent regulation of heterotrimeric G proteins by phosducin. Authors: Gaudet, R. / Savage, J.R. / McLaughlin, J.N. / Willardson, B.M. / Sigler, P.B. #1: ![]() Title: Crystal structure of a G-protein beta gamma dimer at 2.1A resolution. Authors: Sondek, J. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 118.7 KB | Display | ![]() |
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PDB format | ![]() | 91.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b9yC ![]() 2trcS 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: 37430.957 Da / Num. of mol.: 1 / Fragment: LYS-C RESISTANT FRAGMENT, THE BETA SUBUNIT / Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENTS / Source: (natural) ![]() ![]() | ||||
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#2: Protein | Mass: 8040.304 Da / Num. of mol.: 1 Fragment: LYS-C RESISTANT FRAGMENT, THE GAMMA SUBUNIT CLEAVED AFTER RESIDUE 68 Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENTS / Source: (natural) ![]() ![]() | ||||
#3: Protein | Mass: 28204.309 Da / Num. of mol.: 1 / Mutation: S73E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: N-TERMINAL EXTENSION OF THE SEQUENCE MGSSHHHHHHSSGLVPRGSH. Cellular location: CYTOSOLIC / Gene: RAT PDC / Organ: PINEAL GLAND, RETINA / Plasmid: PET15B/S73E / Species (production host): Escherichia coli / Gene (production host): RAT PDC / Production host: ![]() ![]() | ||||
#4: Chemical | ChemComp-GD / #5: Water | ChemComp-HOH / | Compound details | PHOSPHORYLATION SITE S73 IN PHOSDUCIN IS MUTATED TO GLUTAMATE (S73E) IN THIS STRUCTURE BUT IS NOT ...PHOSPHORYL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 13631 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.126 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3→3.09 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.418 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2TRC Resolution: 3→50 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 Details: DISORDERED REGION IN PHOSDUCIN FROM RESIDUE 37 - 38 WAS MODELED STEREOCHEMICALLY AS A POLYALANINE CHAIN. DISORDERED REGION IN PHOSDUCIN FROM RESIDUE 39 - 86 WAS NOT VISIBLE IN THE MAPS AND WAS NOT MODELLED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.07 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. reflection all: 13659 / σ(F): 2 / % reflection Rfree: 9.6 % / Rfactor all: 0.23 / Rfactor obs: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 57.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Rfactor Rfree: 0.316 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.287 / Num. reflection obs: 1754 / Rfactor all: 0.32 / Rfactor obs: 0.287 |