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Yorodumi- PDB-1q8d: The crystal structure of GDNF family co-receptor alpha 1 domain 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q8d | ||||||
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Title | The crystal structure of GDNF family co-receptor alpha 1 domain 3 | ||||||
Components | GDNF family receptor alpha 1GFRα | ||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / all-alpha / cys-rich / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information RET signaling / neurotrophin receptor activity / plasma membrane protein complex / RAF/MAP kinase cascade / multivesicular body / kidney development / neuron differentiation / neuron projection development / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation ...RET signaling / neurotrophin receptor activity / plasma membrane protein complex / RAF/MAP kinase cascade / multivesicular body / kidney development / neuron differentiation / neuron projection development / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / integrin binding / signaling receptor activity / nervous system development / receptor complex / external side of plasma membrane / axon / neuronal cell body / Golgi apparatus / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Leppanen, V.M. / Bespalov, M.M. / Runeberg-Roos, P. / Puurand, U. / Merits, A. / Saarma, M. / Goldman, A. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: The structure of GFRalpha1 domain 3 reveals new insights into GDNF binding and RET activation. Authors: Leppanen, V.M. / Bespalov, M.M. / Runeberg-Roos, P. / Puurand, U. / Merits, A. / Saarma, M. / Goldman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q8d.cif.gz | 30.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q8d.ent.gz | 22.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q8d ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q8d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12075.384 Da / Num. of mol.: 1 / Fragment: Domain 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GFRA1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q62997 |
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#2: Chemical | ChemComp-MPD / ( |
#3: 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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, MES, magnesium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9635 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 30, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED DOUBLE Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9635 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 12986 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 41.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 9.4 / Num. unique all: 1300 / Rsym value: 0.255 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→19.19 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 333127.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4109 Å2 / ksol: 0.351992 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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