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Yorodumi- PDB-2v5e: The structure of the GDNF:Coreceptor complex: Insights into RET s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v5e | |||||||||
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Title | The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding. | |||||||||
Components |
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Keywords | RECEPTOR/GLYCOPROTEIN COMPLEX / RECEPTOR-GLYCOPROTEIN COMPLEX / ALTERNATIVE SPLICING / CELL MEMBRANE / GROWTH FACTOR / LIGAND-CORECEPTOR / GPI-ANCHOR / LIPOPROTEIN / POLYMORPHISM / GLYCOPROTEIN / MEMBRANE / RECEPTOR / SECRETED / GFRALPHA1 / CLEAVAGE ON PAIR OF BASIC RESIDUES / RECEPTOR-GLYCOPROTEIN COMPLEX complex | |||||||||
Function / homology | Function and homology information chemoattractant activity involved in axon guidance / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity ...chemoattractant activity involved in axon guidance / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity / glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / RET signaling / glial cell-derived neurotrophic factor receptor signaling pathway / regulation of morphogenesis of a branching structure / neurotrophin receptor activity / regulation of dopamine uptake involved in synaptic transmission / Formation of the ureteric bud / enteric nervous system development / peristalsis / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of dopamine secretion / sympathetic nervous system development / peripheral nervous system development / organ induction / plasma membrane protein complex / regulation of stem cell differentiation / commissural neuron axon guidance / metanephros development / NCAM1 interactions / mRNA stabilization / RAF/MAP kinase cascade / neural crest cell migration / branching involved in ureteric bud morphogenesis / RET signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / embryonic organ development / multivesicular body / adult locomotory behavior / kidney development / positive regulation of cell differentiation / growth factor activity / neuron differentiation / receptor tyrosine kinase binding / integrin binding / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / cell migration / regulation of gene expression / signaling receptor activity / nervous system development / RAF/MAP kinase cascade / negative regulation of neuron apoptotic process / receptor complex / external side of plasma membrane / axon / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Parkash, V. / Leppanen, V.-M. / Virtanen, H. / Jurvansuu, J.-M. / Bespalov, M.M. / Sidorova, Y.A. / Runeberg-Roos, P. / Saarma, M. / Goldman, A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Structure of the Glial Cell Line-Derived Neurotrophic Factor-Coreceptor Complex: Insights Into Ret Signaling and Heparin Binding. Authors: Parkash, V. / Leppanen, V.-M. / Virtanen, H. / Jurvansuu, J.-M. / Bespalov, M.M. / Sidorova, Y.A. / Runeberg-Roos, P. / 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 | 2v5e.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5e.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v5e_validation.pdf.gz | 1000.8 KB | Display | wwPDB validaton report |
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Full document | 2v5e_full_validation.pdf.gz | 1004.1 KB | Display | |
Data in XML | 2v5e_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 2v5e_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5e ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5e | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 22538.631 Da / Num. of mol.: 1 / Fragment: RESIDUES 150-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PFASTBAC / Cell line (production host): SF9 Production host: SPODOPTERA FRUGIPERDA; EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM (fall armyworm) References: UniProt: Q62997 |
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#2: Protein | Mass: 11430.114 Da / Num. of mol.: 1 / Fragment: RESIDUES 111-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 Production host: SPODOPTERA FRUGIPERDA; EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM (fall armyworm) References: UniProt: P39905 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 227 molecules
#4: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | N-ACETYLGLUCSequence details | THE SEQUENCE NUMBERING OF THE MATURE GDNF EXCLUDES THE 77 RESIDUES OF THE PREPRO REGION FROM THE SEQUENCE. | |
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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: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100MM HEPES PH7.5, 10% PEG-8K, 8% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 190 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20 Å / Num. obs: 19071 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.35→2.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.29 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1AGQ CHAIN A, 2GH0 CHAIN A Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.822 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BECAUSE OF POOR ELECTRON DENSITY, FOLLOWING RESIDUES ATOMS WERE MISSING: ARG A 238 CG CD NE CZ NH1 NH2 LYS B 96 CG CD CE NZ
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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