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Yorodumi- PDB-2wv3: Neuroplastin-55 binds to and signals through the fibroblast growt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wv3 | ||||||
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Title | Neuroplastin-55 binds to and signals through the fibroblast growth factor receptor | ||||||
Components | NEUROPLASTINNPTN | ||||||
Keywords | CELL ADHESION / IGCAM / MEMBRANE / GLYCOPROTEIN / CELL MEMBRANE / TRANSMEMBRANE / DISULFIDE BOND / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information regulation of receptor localization to synapse / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse ...regulation of receptor localization to synapse / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / negative regulation of cytokine production / positive regulation of protein localization / homophilic cell adhesion via plasma membrane adhesion molecules / immunological synapse / regulation of cell adhesion / cell adhesion molecule binding / synaptic membrane / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / axon guidance / synapse organization / visual learning / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / positive regulation of neuron projection development / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / transmembrane transporter binding / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / membrane => GO:0016020 / positive regulation of protein phosphorylation / axon / dendrite / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Soroka, V. / Owczarek, S. / Kastrup, J.S. / Berezin, V. / Bock, E. / Gajhede, M. | ||||||
Citation | Journal: Faseb J. / Year: 2010 Title: Neuroplastin-55 Binds to and Signals Through the Fibroblast Growth Factor Receptor Authors: Owczarek, S. / Kiryushko, D. / Larsen, M.H. / Kastrup, J.S. / Gajhede, M. / Sandi, C. / Berezin, V. / Bock, E. / Soroka, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wv3.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wv3.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2wv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wv3 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wv3 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21585.117 Da / Num. of mol.: 1 / Fragment: IG2 AND IG3 OF NEUROPLASTIN-65, RESIDUES 29-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PPIC9K / Cell line (production host): HIS 4 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P97546 | ||
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#2: Sugar | #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: 2.95 Å3/Da / Density % sol: 57.98 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: NEUROPLASTIN-55 AT A CONCENTRATION OF 4 MG/ML IN 5 MM SODIUM PHOSPHATE AND 150 MM NACL, PH 7.4, WAS MIXED WITH THE RESERVOIR SOLUTION CONTAINING 13-15% W/V PEG 4000, 0.2 M AMMONIUM SULFATE, ...Details: NEUROPLASTIN-55 AT A CONCENTRATION OF 4 MG/ML IN 5 MM SODIUM PHOSPHATE AND 150 MM NACL, PH 7.4, WAS MIXED WITH THE RESERVOIR SOLUTION CONTAINING 13-15% W/V PEG 4000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE, PH 4.6. |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→33.6 Å / Num. obs: 20597 / % possible obs: 99.2 % / Observed criterion σ(I): 1.45 / Redundancy: 7.1 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.95→33.601 Å / SU ML: 0.29 / σ(F): 1.45 / Phase error: 28.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.633 Å2 / ksol: 0.395 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→33.601 Å
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Refine LS restraints |
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LS refinement shell |
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