+Open data
-Basic information
Entry | Database: PDB / ID: 3g5b | ||||||
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Title | The structure of UNC5b cytoplasmic domain | ||||||
Components | Netrin receptor UNC5B | ||||||
Keywords | APOPTOSIS / ZU5 / Death domain / UPA / Developmental protein / Glycoprotein / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane | ||||||
Function / homology | Function and homology information netrin receptor activity / anterior/posterior axon guidance / : / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / negative regulation of neuron apoptotic process / membrane => GO:0016020 / membrane raft / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2 Å | ||||||
Authors | Wang, R. / Wei, Z. / Zhang, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor Authors: Wang, R. / Wei, Z. / Jin, H. / Wu, H. / Yu, C. / Wen, W. / Chan, L.-N. / Wen, Z. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g5b.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g5b.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g5b ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5b | 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: 44586.750 Da / Num. of mol.: 1 / Fragment: UNP residues 541-945 / Mutation: S542G, T744P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc5b / Plasmid: modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O08722 | ||
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#2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.05 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.4~0.5M Ammonium Phosphate, 0.1M MES Buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2007 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 25672 / Num. obs: 25672 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.381 / Num. unique all: 3572 / Rsym value: 0.381 / % possible all: 95.8 |
-Phasing
Phasing | Method: SIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2→27.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.206 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.07 Å2 / Biso mean: 36.747 Å2 / Biso min: 16.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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