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- PDB-6fkq: THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A... -
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Basic information
Entry | Database: PDB / ID: 6fkq | |||||||||
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Title | THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A FRAGMENT OF DRAXIN | |||||||||
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![]() | SIGNALING PROTEIN / AXON GUIDANCE CUE / NETRIN-1 / DRAXIN / COMMISSURAL NEURON | |||||||||
Function / homology | ![]() commissural neuron differentiation in spinal cord / anterior commissure morphogenesis / dorsal spinal cord development / regulation of glial cell migration / chemorepulsion of axon / negative regulation of hippocampal neuron apoptotic process / anterior/posterior axon guidance / hippocampal neuron apoptotic process / Cdc42 protein signal transduction / Role of second messengers in netrin-1 signaling ...commissural neuron differentiation in spinal cord / anterior commissure morphogenesis / dorsal spinal cord development / regulation of glial cell migration / chemorepulsion of axon / negative regulation of hippocampal neuron apoptotic process / anterior/posterior axon guidance / hippocampal neuron apoptotic process / Cdc42 protein signal transduction / Role of second messengers in netrin-1 signaling / Netrin-1 signaling / motor neuron migration / Regulation of commissural axon pathfinding by SLIT and ROBO / negative regulation of axon extension / Netrin mediated repulsion signals / substrate-dependent cell migration, cell extension / mammary gland duct morphogenesis / positive regulation of cell motility / nuclear migration / DCC mediated attractive signaling / regulation of synapse assembly / inner ear morphogenesis / DSCAM interactions / basement membrane / glial cell proliferation / positive regulation of axon extension / positive regulation of glial cell proliferation / forebrain development / substrate adhesion-dependent cell spreading / axon guidance / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / cell-cell adhesion / actin cytoskeleton / Ras protein signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / regulation of transcription by RNA polymerase II / extracellular region / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bhowmick, T. / Meijers, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC. Authors: Ying Liu / Tuhin Bhowmick / Yiqiong Liu / Xuefan Gao / Haydyn D T Mertens / Dmitri I Svergun / Junyu Xiao / Yan Zhang / Jia-Huai Wang / Rob Meijers / ![]() ![]() ![]() Abstract: Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue ...Axon guidance involves the spatiotemporal interplay between guidance cues and membrane-bound cell-surface receptors, present on the growth cone of the axon. Netrin-1 is a prototypical guidance cue that binds to deleted in colorectal cancer (DCC), and it has been proposed that the guidance cue Draxin modulates this interaction. Here, we present structural snapshots of Draxin/DCC and Draxin/Netrin-1 complexes, revealing a triangular relationship that affects Netrin-mediated haptotaxis and fasciculation. Draxin interacts with DCC through the N-terminal four immunoglobulin domains, and Netrin-1 through the EGF-3 domain, in the same region where DCC binds. Netrin-1 and DCC bind to adjacent sites on Draxin, which appears to capture Netrin-1 and tether it to the DCC receptor. We propose the conformational flexibility of the single-pass membrane receptor DCC is used to promote fasciculation and regulate axon guidance through concerted Netrin-1/Draxin binding. VIDEO ABSTRACT. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 106.6 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z5kC ![]() 4urtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 46827.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NETRIN-1 IS A PROTOTYPICAL AXON GUIDANCE CUE THAT BINDS TO THE RECEPTOR DELETED IN COLORECTAL CANCER (DCC). Source: (gene. exp.) ![]() ![]() |
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#2: Protein/peptide | Mass: 2302.597 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 225-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | 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-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose | |
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-Non-polymers , 3 types, 12 molecules ![](data/chem/img/CA.gif)
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#5: Chemical | ChemComp-CA / | ||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GOL / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.62 Å3/Da / Density % sol: 73.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.6 M AMMONIUM SULPHATE AND 0.1 M SODIUM CITRATE, AT PH 4 TO PH 5, VAPOR DIFFUSION, TEMPERATURE 298K PH range: 4-5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.07→54.13 Å / Num. obs: 18063 / % possible obs: 99.9 % / Redundancy: 32.9 % / Rmerge(I) obs: 0.587 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.07→3.23 Å / Redundancy: 18.6 % / Rmerge(I) obs: 2.897 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4URT Resolution: 3.07→54.01 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU B: 23.425 / SU ML: 0.375 / Cross valid method: THROUGHOUT / ESU R: 0.826 / ESU R Free: 0.387 / 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: 76.42 Å2
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Refinement step | Cycle: LAST / Resolution: 3.07→54.01 Å
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