+Open data
-Basic information
Entry | Database: PDB / ID: 4i6p | ||||||
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Title | Crystal structure of Par3-NTD domain | ||||||
Components | Partitioning defective 3 homolog | ||||||
Keywords | SIGNALING PROTEIN / PB1 like motif / DUF3534 / Cell polarity protein | ||||||
Function / homology | Function and homology information Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / lateral loop / positive regulation of myelination ...Tight junction interactions / regulation of actin filament-based process / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / internode region of axon / regulation of cellular localization / PAR polarity complex / apical constriction / establishment of centrosome localization / lateral loop / positive regulation of myelination / establishment of epithelial cell polarity / Schmidt-Lanterman incisure / bicellular tight junction assembly / myelination in peripheral nervous system / phosphatidylinositol-3-phosphate binding / establishment or maintenance of epithelial cell apical/basal polarity / protein targeting to membrane / wound healing, spreading of cells / apical junction complex / centrosome localization / establishment of cell polarity / negative regulation of peptidyl-threonine phosphorylation / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / bicellular tight junction / endomembrane system / axonal growth cone / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / adherens junction / microtubule cytoskeleton organization / spindle / cell-cell junction / protein localization / cell junction / apical part of cell / cell cortex / protein phosphatase binding / cell adhesion / apical plasma membrane / cell division / neuronal cell body / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wang, W. / Gao, F. / Gong, W. / Sun, F. / Feng, W. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural insights into the intrinsic self-assembly of Par-3 N-terminal domain. Authors: Yan Zhang / Wenjuan Wang / Jia Chen / Kai Zhang / Feng Gao / Bingquan Gao / Shuai Zhang / Mingdong Dong / Flemming Besenbacher / Weimin Gong / Mingjie Zhang / Fei Sun / Wei Feng / Abstract: Par-3, the central organizer of the Par-3/Par-6/atypical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal ...Par-3, the central organizer of the Par-3/Par-6/atypical protein kinase C complex, is a multimodular scaffold protein that is essential for cell polarity establishment and maintenance. The N-terminal domain (NTD) of Par-3 is capable of self-association to form filament-like structures, although the underlying mechanism is poorly understood. Here, we determined the crystal structure of Par-3 NTD and solved the filament structure by cryoelectron microscopy. We found that an intrinsic "front-to-back" interaction mode is important for Par-3 NTD self-association and that both the lateral and longitudinal packing within the filament are mediated by electrostatic interactions. Disruptions of the lateral or longitudinal packing significantly impaired Par-3 NTD self-association and thereby impacted the Par-3-mediated epithelial polarization. We finally demonstrated that a Par-3 NTD-like domain from histidine ammonia-lyase also harbors a similar self-association capacity. This work unequivocally provides the structural basis for Par-3 NTD self-association and characterizes one type of protein domain that can self-assemble via electrostatic interactions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6p.cif.gz | 46 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6p.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 4i6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6p ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6p | HTTPS FTP |
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-Related structure data
Related structure data | 2237C 3zeeC 2ns5S 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | This protein forms helical filament in solution. Cryo-electron microscopic reconstruction revealed that the dimer in the crystallographic asymmetric unit is the same as the building block of the helical filament. |
-Components
#1: Protein | Mass: 9879.212 Da / Num. of mol.: 2 / Fragment: N-terminal domain of Par3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pard3, Par3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus / References: UniProt: Q9Z340 #2: 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: 3.5 Å3/Da / Density % sol: 64.84 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6 M ammonium sulfate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 1, 2010 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 6597 / Num. obs: 6406 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.6 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 5.3 / Num. unique all: 617 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NS5 Resolution: 2.9→39.94 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 19.255 / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.008 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 55.809 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→39.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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