[English] 日本語
Yorodumi- PDB-5jgq: X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jgq | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand. | ||||||
Components | Neuropilin-1 | ||||||
Keywords | SIGNALING PROTEIN / Neuropilin-1 / Angiogenesis | ||||||
Function / homology | Function and homology information endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis ...endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / 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 / neurofilament / postsynapse organization / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / motor neuron migration / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / CHL1 interactions / vascular endothelial growth factor receptor activity / regulation of vesicle-mediated transport / Signaling by ROBO receptors / angiogenesis involved in coronary vascular morphogenesis / neuropilin signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / coronary artery morphogenesis / hepatocyte growth factor receptor signaling pathway / substrate-dependent cell migration, cell extension / outflow tract septum morphogenesis / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / semaphorin receptor complex / cell migration involved in sprouting angiogenesis / axonal fasciculation / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / positive chemotaxis / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / GTPase activator activity / Signal transduction by L1 / integrin-mediated signaling pathway / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / axon guidance / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / symbiont entry into host cell Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Fotinou, C. / Rana, R. / Djordjevic, S. / Yelland, T. | ||||||
Citation | Journal: FEBS J. / Year: 2018 Title: Architecture and hydration of the arginine-binding site of neuropilin-1. Authors: Mota, F. / Fotinou, C. / Rana, R.R. / Chan, A.W.E. / Yelland, T. / Arooz, M.T. / O'Leary, A.P. / Hutton, J. / Frankel, P. / Zachary, I. / Selwood, D. / Djordjevic, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5jgq.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jgq.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 5jgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jgq_validation.pdf.gz | 712 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5jgq_full_validation.pdf.gz | 712.3 KB | Display | |
Data in XML | 5jgq_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5jgq_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jgq ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jgq | HTTPS FTP |
-Related structure data
Related structure data | 5ijrC 5iyyC 5j1xC 5jgiC 5jhkC 1kexS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 274 - 426 / Label seq-ID: 5 - 157
|
-Components
#1: Protein | Mass: 17917.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Plasmid: pET15B-TEV-NRP1B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami2 (DE3)pLysS / References: UniProt: O14786 #2: Chemical | ChemComp-DMS / | #3: Chemical | ChemComp-6JY / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.04 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 18%PEG3350+0.2M NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.92 Å / Num. obs: 37578 / % possible obs: 97 % / Redundancy: 3.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 2 / % possible all: 75.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1kex Resolution: 1.6→44.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.589 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.591 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|