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Yorodumi- PDB-5iyy: X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iyy | ||||||
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Title | X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand. | ||||||
Components | Neuropilin-1 | ||||||
Keywords | SIGNALING PROTEIN / Neuropilin-1 / Angiogenesis | ||||||
Function / homology | Function and homology information endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis ...endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / neurofilament / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / postsynapse organization / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / negative regulation of axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / axonogenesis involved in innervation / CHL1 interactions / vascular endothelial growth factor receptor activity / outflow tract septum morphogenesis / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / angiogenesis involved in coronary vascular morphogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / axonal fasciculation / cell migration involved in sprouting angiogenesis / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / neural crest cell migration / sprouting angiogenesis / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive chemotaxis / cytokine binding / growth factor binding / positive regulation of smooth muscle cell migration / sorting endosome / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / semaphorin-plexin signaling pathway / 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 / axon guidance / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / mitochondrial membrane / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / postsynaptic membrane / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / early endosome / Attachment and Entry / receptor complex / neuron projection 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iyy.cif.gz | 145.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iyy.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 5iyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iyy_validation.pdf.gz | 878.6 KB | Display | wwPDB validaton report |
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Full document | 5iyy_full_validation.pdf.gz | 881.6 KB | Display | |
Data in XML | 5iyy_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5iyy_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/5iyy ftp://data.pdbj.org/pub/pdb/validation_reports/iy/5iyy | HTTPS FTP |
-Related structure data
Related structure data | 5ijrC 5j1xC 5jgiC 5jgqC 5jhkC 1kexS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 272 - 426 / Label seq-ID: 3 - 157
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-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 / Details (production host): pET15b-TEV-nrp1b1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami2-pLysS / References: UniProt: O14786 #2: Chemical | #3: 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: 2.17 Å3/Da / Density % sol: 43.23 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 30% w/v PEG3350, 0.2 M AmCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 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: 1.38→41.5 Å / Num. obs: 60739 / % possible obs: 98 % / Redundancy: 6.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.4 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KEX Resolution: 1.6→44.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.901 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.416 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→44.47 Å
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