+Open data
-Basic information
Entry | Database: PDB / ID: 5o0n | |||||||||
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Title | Deglycosylated Nogo Receptor with native disulfide structure 4 | |||||||||
Components | Reticulon-4 receptor | |||||||||
Keywords | SIGNALING PROTEIN / nervous system / signaling / leucine-rich repeat domain / disulfide structure | |||||||||
Function / homology | Function and homology information Roundabout binding / 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 / corpus callosum development / negative chemotaxis ...Roundabout binding / 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 / corpus callosum development / negative chemotaxis / positive regulation of Rho protein signal transduction / axonal growth cone / axonogenesis / positive regulation of GTPase activity / dendritic shaft / axon guidance / presynapse / negative regulation of neuron projection development / signaling receptor activity / heparin binding / growth cone / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Pronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C. | |||||||||
Funding support | Netherlands, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction. Authors: Pronker, M.F. / Tas, R.P. / Vlieg, H.C. / Janssen, B.J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o0n.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o0n.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 5o0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o0n_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5o0n_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5o0n_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5o0n_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/5o0n ftp://data.pdbj.org/pub/pdb/validation_reports/o0/5o0n | HTTPS FTP |
-Related structure data
Related structure data | 5o0kC 5o0lC 5o0mC 5o0oC 5o0pC 5o0qC 5o0rC 1oznS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36011.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rtn4r, Ngr1, Nogor / Plasmid: pUPE107.03 / Details (production host): secretion signal peptide, / Cell line (production host): HEK293 / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / Variant (production host): GntI-/- / References: UniProt: Q99PI8 |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 8 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM ...Details: Co-crystallization trial with mouse Nogo54, an extracellular construct derived from the NgR ligand Nogo-A (UNIPROT Q99P72, residues 1025-1078). Nogo54 was purified in 150 mM NaCl, 20 mM HEPES pH 7.0 at a concentration of 3.3 mg/mL and mixed in a 1:1 molar ratio with Endo-Hf-deglycosylated NgRa at a concentration of 10 mg/mL. Crystals were grown in a condition of 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90.63 Å / Num. obs: 13084 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rsym value: 0.066 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.704 / Rsym value: 0.912 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OZN Resolution: 2.5→90.63 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→90.63 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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