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Yorodumi- PDB-1tad: GTPASE MECHANISM OF GPROTEINS FROM THE 1.7-ANGSTROM CRYSTAL STRUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tad | ||||||
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Title | GTPASE MECHANISM OF GPROTEINS FROM THE 1.7-ANGSTROM CRYSTAL STRUCTURE OF TRANSDUCIN ALPHA-GDP-ALF4- | ||||||
Components | TRANSDUCIN-ALPHA | ||||||
Keywords | GTP-BINDING PROTEIN / G-PROTEIN / GTPASE / TRANSDUCIN | ||||||
Function / homology | Function and homology information negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment ...negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment / visual perception / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / GTP binding / protein kinase binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Sondek, J. / Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B. | ||||||
Citation | Journal: Nature / Year: 1994 Title: GTPase mechanism of Gproteins from the 1.7-A crystal structure of transducin alpha-GDP-AIF-4. Authors: Sondek, J. / Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B. #1: Journal: Nature / Year: 1994 Title: Structural Determinants for Activation of the Alpha-Subunit of a Heterotrimeric G Protein Authors: Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B. #2: Journal: Nature / Year: 1993 Title: The 2.2 Angstroms Crystal Structure of Transducin-Alpha Complexed with GTP-Gamma-S Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tad.cif.gz | 231.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tad.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/1tad ftp://data.pdbj.org/pub/pdb/validation_reports/ta/1tad | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: RESIDUES CAC A 353, CAC B 353, AND CAC C 353 MODIFY RESIDUES CYS A 62, CYS B 62, AND CYS C 62, RESPECTIVELY. 2: RESIDUES CAC A 354, CAC B 354, AND CAC C 354 MODIFY RESIDUES CYS A 210, CYS B 210, AND CYS C 210, RESPECTIVELY. | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE THREE COMPLEXES OF TRANSDUCIN ALPHA, GDP, ALUMINUM FLUORIDE, AND CA 2+ PER ASYMMETRIC UNIT. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 C 30 .. C 340 B 30 .. B 340 0.252 M2 C 30 .. C 340 A 30 .. A 340 0.353 M3 B 30 .. B 340 A 30 .. A 340 0.404 |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 37141.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Tissue: RETINA / Organ: EYE / References: UniProt: P04695 |
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-Non-polymers , 5 types, 1029 molecules
#2: Chemical | #3: Chemical | ChemComp-CAC / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CAC IS DIMETHYL ARSENIC OXIDE, DERIVED FROM CRYSTALLIZATION BUFFER. ALSO KNOWN AS DIMETHYLARSINIC ...CAC IS DIMETHYL ARSENIC OXIDE, DERIVED FROM CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95 Å |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Feb 11, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Num. obs: 116584 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.78 Å / % possible obs: 76.7 % / Redundancy: 4.22 % / Num. unique obs: 12535 / Rmerge(I) obs: 0.186 |
-Processing
Software |
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Refinement | Resolution: 1.7→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor all: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |