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Yorodumi- PDB-6tjt: Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tjt | ||||||
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Title | Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / VEGF-binding / NRP2 / angiogenesis / immunomodulation | ||||||
Function / homology | Function and homology information positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development ...positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 3 binding / substrate-dependent cell migration / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / axon extension involved in axon guidance / positive regulation of mesenchymal stem cell proliferation / NrCAM interactions / morphogenesis of embryonic epithelium / sympathetic neuron projection extension / Neurophilin interactions with VEGF and VEGFR / sympathetic ganglion development / VEGF binds to VEGFR leading to receptor dimerization / neural crest cell migration involved in autonomic nervous system development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / induction of positive chemotaxis / outflow tract septum morphogenesis / semaphorin receptor activity / sprouting angiogenesis / regulation of postsynapse organization / vascular endothelial growth factor signaling pathway / negative chemotaxis / positive regulation of neuroblast proliferation / cytokine binding / chemoattractant activity / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of cell division / negative regulation of osteoblast differentiation / positive regulation of blood vessel endothelial cell migration / glial cell proliferation / vascular endothelial growth factor receptor signaling pathway / positive regulation of glial cell proliferation / positive regulation of protein autophosphorylation / negative regulation of blood pressure / positive regulation of endothelial cell proliferation / cellular response to leukemia inhibitory factor / positive regulation of endothelial cell migration / platelet alpha granule lumen / axon guidance / positive regulation of protein secretion / animal organ morphogenesis / growth factor activity / positive regulation of angiogenesis / Platelet degranulation / signaling receptor activity / heparin binding / postsynaptic membrane / angiogenesis / response to hypoxia / cell adhesion / response to xenobiotic stimulus / positive regulation of protein phosphorylation / axon / glutamatergic synapse / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Eldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S. | ||||||
Citation | Journal: To Be Published Title: NRP2-b1 domain in a complex with the C-terminal VEGFC peptide Authors: Eldrid, C. / Yu, L. / Yelland, T. / Fotinou, C. / Djordjevic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tjt.cif.gz | 184.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tjt.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjt ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjt | HTTPS FTP |
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-Related structure data
Related structure data | 4rn5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18368.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first N-terminal residue and the last two C-terminal residues from the protein construct were not observed in the electron density maps. Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Escherichia coli (E. coli) / References: UniProt: O60462 #2: Protein/peptide | Mass: 671.834 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The electron density for the acetylated N-terminal Ser and the two Ile residues did not allow for the modeling of these residues. Source: (synth.) Homo sapiens (human) / References: UniProt: P49767*PLUS #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M NaOAc, 0.1 M HEPES pH 7.5, 12 % (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å | ||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2016 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.31→63 Å / Num. obs: 86786 / % possible obs: 98.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.52 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.6 | ||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RN5 Resolution: 1.31→48.64 Å / SU ML: 0.1122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0195
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→48.64 Å
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Refine LS restraints |
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LS refinement shell |
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