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Yorodumi- PDB-4pam: A conserved phenylalanine as relay between the 5 helix and the GD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pam | ||||||||||||||||||||||||||||||
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Title | A conserved phenylalanine as relay between the 5 helix and the GDP binding region of heterotrimeric G protein | ||||||||||||||||||||||||||||||
Components | Guanine nucleotide-binding protein G(i) subunit alpha-1 | ||||||||||||||||||||||||||||||
Keywords | SIGNALING PROTEIN / Activation of Heterotrimeric G protein / GDP release / Computer modeling / G protein Coupled Receptors / Rhodopsin | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding ...Extra-nuclear estrogen signaling / Adenylate cyclase inhibitory pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / negative regulation of synaptic transmission / GTPase activating protein binding / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / GDP binding / heterotrimeric G-protein complex / cell cortex / midbody / cell cycle / G protein-coupled receptor signaling pathway / cell division / GTPase activity / centrosome / GTP binding / magnesium ion binding / protein-containing complex / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å | ||||||||||||||||||||||||||||||
Authors | Kaya, A.I. / Lokits, A.D. / Gilbert, J. / Iverson, T.M. / Meiler, J. / Hamm, H.E. | ||||||||||||||||||||||||||||||
Funding support | United States, 9items
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Citation | Journal: J.Biol.Chem. / Year: 2014 Title: A Conserved Phenylalanine as a Relay between the alpha 5 Helix and the GDP Binding Region of Heterotrimeric Gi Protein alpha Subunit. Authors: Kaya, A.I. / Lokits, A.D. / Gilbert, J.A. / Iverson, T.M. / Meiler, J. / Hamm, H.E. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pam.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pam.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pam ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pam | HTTPS FTP |
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-Related structure data
Related structure data | 4panC 4paoC 4paqC 1gddS 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
#1: Protein | Mass: 40355.000 Da / Num. of mol.: 1 / Mutation: F336C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gnai1, Gnai-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10824 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-SO3 / |
#4: Chemical | ChemComp-CL / |
#5: 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: 3.1 Å3/Da / Density % sol: 60.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: (NH4)2SO3, Sodium acetate / PH range: 5.9-6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34 Å / Num. obs: 28903 / % possible obs: 99 % / Redundancy: 4 % / Rsym value: 0.053 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.379 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GDD Resolution: 2.101→34.093 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.101→34.093 Å
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Refine LS restraints |
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LS refinement shell |
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