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- PDB-4uu5: CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF PALS1 IN COMPLEX WITH THE ... -
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Basic information
Entry | Database: PDB / ID: 4uu5 | |||||||||
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Title | CRYSTAL STRUCTURE OF THE PDZ DOMAIN OF PALS1 IN COMPLEX WITH THE CRB PEPTIDE | |||||||||
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![]() | CELL ADHESION | |||||||||
Function / homology | ![]() post-embryonic retina morphogenesis in camera-type eye / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / photoreceptor cell outer segment organization / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of transforming growth factor beta receptor signaling pathway ...post-embryonic retina morphogenesis in camera-type eye / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / photoreceptor cell outer segment organization / morphogenesis of an epithelial sheet / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / regulation of transforming growth factor beta receptor signaling pathway / eye photoreceptor cell development / plasma membrane organization / lateral loop / myelin sheath adaxonal region / glial cell differentiation / Schmidt-Lanterman incisure / photoreceptor cell maintenance / establishment or maintenance of epithelial cell apical/basal polarity / peripheral nervous system myelin maintenance / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / establishment or maintenance of cell polarity / generation of neurons / central nervous system neuron development / microvillus / bicellular tight junction / blood vessel remodeling / visual perception / photoreceptor inner segment / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / cerebral cortex development / cell-cell signaling / gene expression / perikaryon / membrane => GO:0016020 / apical plasma membrane / protein domain specific binding / axon / calcium ion binding / Golgi apparatus / protein-containing complex / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ivanova, M.E. / Purkiss, A.G. / McDonald, N.Q. | |||||||||
![]() | ![]() Title: Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove. Authors: Ivanova, M.E. / Fletcher, G.C. / O'Reilly, N. / Purkiss, A.G. / Thompson, B.J. / McDonald, N.Q. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 47 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uu6C ![]() 1va8S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 9650.056 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN, RESIDUES 251-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2101.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1390-1406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 130 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PUN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PUN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-PUN / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 251-335 N-TERMINAL RESIDUES GPLGS ARE VECTOR- DERIVED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.37 % Description: MODEL WAS GENERATED BY PHYRE SERVER BASED ON 1VA8 |
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES (PH 7.29), 2.68M NA CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→52.84 Å / Num. obs: 35567 / % possible obs: 99.7 % / Observed criterion σ(I): 1.9 / Redundancy: 6.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.23→1.26 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VA8 Resolution: 1.23→52.842 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 16.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→52.842 Å
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Refine LS restraints |
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LS refinement shell |
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