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Yorodumi- PDB-6fkq: THE CRYSTAL STRUCTURE OF A FRAGMENT OF NETRIN-1 IN COMPLEX WITH A... -
+Open data
-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 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / AXON GUIDANCE CUE / NETRIN-1 / DRAXIN / COMMISSURAL NEURON | |||||||||
Function / homology | Function and homology information commissural neuron differentiation in spinal cord / anterior commissure morphogenesis / dorsal spinal cord development / regulation of glial cell migration / chemorepulsion of axon / DSCAM interactions / negative regulation of hippocampal neuron apoptotic process / anterior/posterior axon guidance / hippocampal neuron apoptotic process / Cdc42 protein signal transduction ...commissural neuron differentiation in spinal cord / anterior commissure morphogenesis / dorsal spinal cord development / regulation of glial cell migration / chemorepulsion of axon / DSCAM interactions / 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 / nuclear migration / positive regulation of cell motility / DCC mediated attractive signaling / inner ear morphogenesis / regulation of synapse assembly / positive regulation of glial cell proliferation / basement membrane / glial cell proliferation / positive regulation of axon extension / forebrain development / axon guidance / cell-cell adhesion / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / 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 / regulation of transcription by RNA polymerase II / apoptotic process / extracellular region / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å | |||||||||
Authors | Bhowmick, T. / Meijers, R. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Neuron / Year: 2018 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fkq.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fkq.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fkq_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6fkq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6fkq_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 6fkq_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkq ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkq | HTTPS FTP |
-Related structure data
Related structure data | 5z5kC 4urtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: NTN1, NTN1L / Plasmid: PXLG / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: O95631 |
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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.) Homo sapiens (human) / Gene: DRAXIN, C1orf187, PSEC0258, UNQ3119/PRO10268 / Plasmid: PXLG / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Tissue (production host): KIDNEY / References: UniProt: Q8NBI3 |
-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
#5: Chemical | ChemComp-CA / | ||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GOL / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.987 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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Refine LS restraints |
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