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Yorodumi- PDB-1ozn: 1.5A Crystal Structure of the Nogo Receptor Ligand Binding Domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ozn | |||||||||
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Title | 1.5A Crystal Structure of the Nogo Receptor Ligand Binding Domain Reveals a Convergent Recognition Scaffold Mediating Inhibition of Myelination | |||||||||
Components | Reticulon 4 receptor | |||||||||
Keywords | SIGNALING PROTEIN / Nogo Receptor / MAD / Myelination Inhibition / Omgp / MAG / nogo-66 / p75 / Signal Transduction / Neuronal Regeneration / Ligand Binding | |||||||||
Function / homology | Function and homology information neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction ...neuronal signal transduction / ganglioside GM1 binding / chondroitin sulfate binding / neuregulin receptor activity / ganglioside GT1b binding / negative regulation of axon regeneration / negative regulation of axon extension / Axonal growth inhibition (RHOA activation) / corpus callosum development / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / positive regulation of GTPase activity / dendritic shaft / presynapse / negative regulation of neuron projection development / signaling receptor activity / heparin binding / perikaryon / cell surface receptor signaling pathway / neuron projection / membrane raft / external side of plasma membrane / neuronal cell body / glutamatergic synapse / protein-containing complex binding / cell surface / endoplasmic reticulum / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.52 Å | |||||||||
Authors | He, X. / Bazan, J.F. / Park, J.B. / McDermott, G. / He, Z. / Garcia, K.C. | |||||||||
Citation | Journal: Neuron / Year: 2003 Title: Structure of the Nogo Receptor Ectodomain. A Recognition module implicated in Myelin Inhibition. Authors: He, X.L. / Bazan, J.F. / McDermott, G. / Park, J.B. / Wang, K. / Tessier-Lavigne, M. / He, Z. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ozn.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ozn.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ozn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ozn_validation.pdf.gz | 525 KB | Display | wwPDB validaton report |
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Full document | 1ozn_full_validation.pdf.gz | 528.4 KB | Display | |
Data in XML | 1ozn_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ozn_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/1ozn ftp://data.pdbj.org/pub/pdb/validation_reports/oz/1ozn | HTTPS FTP |
-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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Details | The Nogo Receptor ligand binding domain binds myelin inhibtors such as Nogo, Omgp and MAG |
-Components
#1: Protein | Mass: 31613.375 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTN4R OR NOGOR / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9BZR6 | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | #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: 1.87 Å3/Da / Density % sol: 34.21 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG4000, sodium chloride, sodium acetate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0064, 1.0096, 0.9950 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.52→50 Å / Num. all: 33484 / Num. obs: 33484 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34 | ||||||||||||
Reflection shell | Resolution: 1.52→1.56 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 7.4 / % possible all: 96.4 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å | ||||||||||||
Reflection shell | *PLUS % possible obs: 96.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.52→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.62 Å / Rfactor Rfree error: 0.017
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.56 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226 |