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Yorodumi- PDB-2p4r: Structural basis for a novel interaction between AIP4 and beta-PIX -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p4r | ||||||
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Title | Structural basis for a novel interaction between AIP4 and beta-PIX | ||||||
Components |
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Keywords | LIGASE / SH3 domain peptide ligand complex | ||||||
Function / homology | Function and homology information presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of protein deubiquitination / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / regulation of protein deubiquitination / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / RHOA GTPase cycle / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / T cell anergy / positive regulation of T cell anergy / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / CXCR chemokine receptor binding / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / gamma-tubulin binding / regulation of hematopoietic stem cell differentiation / lamellipodium assembly / negative regulation of type I interferon production / small GTPase-mediated signal transduction / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / mitotic spindle pole / Golgi organization / ubiquitin-like protein ligase binding / protein monoubiquitination / ligase activity / protein K63-linked ubiquitination / Rho protein signal transduction / GABA-ergic synapse / protein autoubiquitination / protein K48-linked ubiquitination / hematopoietic progenitor cell differentiation / ribonucleoprotein complex binding / ruffle / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / guanyl-nucleotide exchange factor activity / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / receptor internalization / Regulation of necroptotic cell death / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / early endosome membrane / growth cone / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / neuron projection / symbiont entry into host cell / inflammatory response / positive regulation of apoptotic process / intracellular membrane-bounded organelle / focal adhesion / innate immune response / centrosome / neuronal cell body / apoptotic process / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Min, K.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: A novel interaction between atrophin-interacting protein 4 and beta-p21-activated kinase-interactive exchange factor is mediated by an SH3 domain. Authors: Janz, J.M. / Sakmar, T.P. / Min, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p4r.cif.gz | 30 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p4r.ent.gz | 19 KB | Display | PDB format |
PDBx/mmJSON format | 2p4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/2p4r ftp://data.pdbj.org/pub/pdb/validation_reports/p4/2p4r | HTTPS FTP |
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-Related structure data
Related structure data | 2ak5S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6731.333 Da / Num. of mol.: 1 / Fragment: Beta-PIX SH3 (10-63) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef7 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O55043 |
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#2: Protein/peptide | Mass: 2698.135 Da / Num. of mol.: 1 / Fragment: AIP4 (209-224) / Source method: obtained synthetically Details: Chemically synthesized. Occurs naturally in humans (homo sapien). References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 1.99 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 11, 2006 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.15 Å / Num. all: 5612 / Num. obs: 5610 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 19.6 Å2 / Rsym value: 0.083 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 17.2 / Num. unique all: 519 / Rsym value: 18.7 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2AK5 Resolution: 2.001→20.87 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.217 / SU B: 4.08 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.178 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.481 Å2
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Refinement step | Cycle: LAST / Resolution: 2.001→20.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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