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Yorodumi- PDB-4g69: Structure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis... -
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-Basic information
Entry | Database: PDB / ID: 4g69 | ||||||
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Title | Structure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis Coli Cytoskeletal Polarity Complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/SIGNALING PROTEIN / PDZ / MAGUK / Polarity / Adenomatous Polyposis Coli / Tetramethylrhodamine / Adherens Junction / MEMBRANE PROTEIN-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / APC truncation mutants are not K63 polyubiquitinated / membrane raft organization / regulation of microtubule-based movement / hard palate development / negative regulation of cell cycle G1/S phase transition / establishment of centrosome localization / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / embryonic skeletal system morphogenesis / astral microtubule organization / gamma-catenin binding / structural constituent of postsynaptic density / NrCAM interactions / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath abaxonal region / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / peristalsis / cell projection membrane / positive regulation of protein localization to centrosome / Synaptic adhesion-like molecules / smooth muscle tissue development / pattern specification process / bicellular tight junction assembly / positive regulation of potassium ion transport / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of microtubule depolymerization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / node of Ranvier / beta-catenin destruction complex / regulation of ventricular cardiac muscle cell action potential / heart valve development / regulation of microtubule-based process / protein-containing complex localization / Trafficking of AMPA receptors / microtubule plus-end binding / protein kinase regulator activity / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / Wnt signalosome / amyloid precursor protein metabolic process / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / cell fate specification / endothelial cell proliferation / lens development in camera-type eye / Activation of Ca-permeable Kainate Receptor / regulation of myelination / cortical actin cytoskeleton organization / endocardial cushion morphogenesis / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / dynein complex binding / positive regulation of actin filament polymerization / mitotic spindle assembly checkpoint signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Apoptotic cleavage of cellular proteins / Unblocking of NMDA receptors, glutamate binding and activation / regulation of cell differentiation / receptor clustering / cytoplasmic microtubule / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / intercalated disc / mitotic cytokinesis / basement membrane / lateral plasma membrane / potassium channel regulator activity / bicellular tight junction / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell proliferation / negative regulation of T cell proliferation / cytoskeletal protein binding / Ras activation upon Ca2+ influx through NMDA receptor / actin filament polymerization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / protein localization to plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Slep, K.C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structure of the Human Discs Large 1 PDZ2- Adenomatous Polyposis Coli Cytoskeletal Polarity Complex: Insight into Peptide Engagement and PDZ Clustering. Authors: Slep, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g69.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g69.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 4g69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g69_validation.pdf.gz | 413.3 KB | Display | wwPDB validaton report |
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Full document | 4g69_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 4g69_validation.xml.gz | 7 KB | Display | |
Data in CIF | 4g69_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/4g69 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/4g69 | HTTPS FTP |
-Related structure data
Related structure data | 2fe5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10600.230 Da / Num. of mol.: 1 / Fragment: PDZ2, UNP residues 310-407 Source method: isolated from a genetically manipulated source Details: GST N-terminal fusion, GST cleaved via Thrombin treatment Source: (gene. exp.) Homo sapiens (human) / Gene: DLG1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q12959 |
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#2: Protein/peptide | Mass: 1207.338 Da / Num. of mol.: 1 / Fragment: APC C-terminal peptide, UNP residues 2833-2843 / Source method: obtained synthetically Details: Adenomatous Polyposis Coli (APC) C-terminal 11 residues synthesized with N-terminal Tetramethyl rhodamine tag Source: (synth.) Homo sapiens (human) / References: UniProt: P25054 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well ...Details: Protein solution: 1.4 mM Dlg1 PDZ2, 1.7 mM APC, 100 mM NaCl, 25 mM Tris pH 7.0, 0.1% B-ME Well: 200 mM sodium acetate, 100 mM sodium cacodylate pH 6.25, 28% PEG 8000 Drop = 1:1 protein:well solution , VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2007 |
Radiation | Monochromator: collected at 1.127 A / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2→70 Å / Num. all: 7000 / Num. obs: 6846 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.07 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 590 / Rsym value: 0.22 / % possible all: 82.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FE5 Resolution: 2→29.379 Å / SU ML: 0.17 / σ(F): 0.1 / Phase error: 15.05 / 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 / Bsol: 32.336 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→29.379 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.1675 Å / Origin y: -4.9337 Å / Origin z: 14.8774 Å
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Refinement TLS group | Selection details: all |