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- PDB-5emb: Crystal structure of the SNX27 PDZ domain bound to the C-terminal... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5emb | ||||||
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Title | Crystal structure of the SNX27 PDZ domain bound to the C-terminal phosphorylated PTHR PDZ binding motif | ||||||
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![]() | PROTEIN TRANSPORT / Endosome / PDZ domain / sorting nexin | ||||||
Function / homology | ![]() response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / neurotransmitter receptor transport to plasma membrane / parathyroid hormone receptor activity / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / G protein-coupled peptide receptor activity ...response to methamphetamine hydrochloride / establishment of protein localization to plasma membrane / positive regulation of AMPA glutamate receptor clustering / neurotransmitter receptor transport to plasma membrane / parathyroid hormone receptor activity / WASH complex / endosome to plasma membrane protein transport / retromer complex / phosphatidylinositol-3-phosphate binding / G protein-coupled peptide receptor activity / endocytic recycling / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / endosomal transport / bone mineralization / regulation of postsynaptic membrane neurotransmitter receptor levels / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / immunological synapse / chondrocyte differentiation / cell maturation / bone resorption / phosphatidylinositol binding / cellular response to nerve growth factor stimulus / skeletal system development / intracellular protein transport / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / calcium-dependent protein binding / : / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / early endosome membrane / G alpha (s) signalling events / basolateral plasma membrane / in utero embryonic development / cell population proliferation / cell surface receptor signaling pathway / early endosome / receptor complex / endosome / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / glutamatergic synapse / positive regulation of cell population proliferation / signal transduction / protein homodimerization activity / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Collins, B.M. / Clairfeuille, T. | ||||||
![]() | ![]() Title: A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex. Authors: Clairfeuille, T. / Mas, C. / Chan, A.S. / Yang, Z. / Tello-Lafoz, M. / Chandra, M. / Widagdo, J. / Kerr, M.C. / Paul, B. / Merida, I. / Teasdale, R.D. / Pavlos, N.J. / Anggono, V. / Collins, B.M. | ||||||
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 | ![]() | 45.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.2 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5elqC ![]() 5em9C ![]() 5emaC ![]() 4z8jS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 10569.952 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 39-133) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1089.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 10% PEG1000, 10% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7085 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→31.265 Å / Num. obs: 90806 / % possible obs: 98.7 % / Redundancy: 14 % / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 0.85→0.86 Å / Redundancy: 13.9 % / Rmerge(I) obs: 2.06 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z8J Resolution: 0.85→10.2 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.275 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.012 / 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: 10.849 Å2
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Refinement step | Cycle: LAST / Resolution: 0.85→10.2 Å
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Refine LS restraints |
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