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Yorodumi- PDB-2nq3: Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiq... -
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-Basic information
Entry | Database: PDB / ID: 2nq3 | ||||||
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Title | Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase | ||||||
Components | Itchy homolog E3 ubiquitin protein ligase | ||||||
Keywords | LIGASE / C2 DOMAIN / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition 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 / CXCR chemokine receptor binding / regulation of necroptotic process ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition 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 / 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 / HECT-type E3 ubiquitin transferase / negative regulation of JNK cascade / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon production / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / protein monoubiquitination / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / ligase activity / protein K48-linked ubiquitination / protein autoubiquitination / ribonucleoprotein complex binding / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / receptor internalization / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / early endosome membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / inflammatory response / symbiont entry into host cell / intracellular membrane-bounded organelle / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. #1: Journal: Genomics / Year: 2001 Title: Human ITCH is a coregulator of the hematopoietic transcription factor NF-E2 Authors: Chen, X. / Wen, S. / Fukuda, M.N. / Gavva, N.R. / Hsu, D. / Akama, T.O. / Yang-Feng, T. / Shen, C.K. #2: Journal: Mol.Cell.Neurosci. / Year: 1998 Title: Atrophin-1, the DRPLA gene product, interacts with two families of WW domain-containing proteins Authors: Wood, J.D. / Yuan, J. / Margolis, R.L. / Colomer, V. / Duan, K. / Kushi, J. / Kaminsky, Z. / Kleiderlein, J.J. / Sharp, A.H. / Ross, C.A. #3: Journal: Mol.Cell.Biol. / Year: 2000 Title: Latent membrane protein 2A of Epstein-Barr virus binds WW domain E3 protein-ubiquitin ligases that ubiquitinate B-cell tyrosine kinases Authors: Winberg, G. / Matskova, L. / Chen, F. / Plant, P. / Rotin, D. / Gish, G. / Ingham, R. / Ernberg, I. / Pawson, T. #4: Journal: J.Biol.Chem. / Year: 2002 Title: Interaction between two ubiquitin-protein isopeptide ligases of different classes, CBLC and AIP4/ITCH Authors: Courbard, J.R. / Fiore, F. / Adelaide, J. / Borg, J.P. / Birnbaum, D. / Ollendorff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nq3.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nq3.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nq3 ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nq3 | HTTPS FTP |
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-Related structure data
Related structure data | 2fk9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19201.719 Da / Num. of mol.: 1 / Fragment: C2 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: p28a-LIC-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-CL / |
#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: 3.34 Å3/Da / Density % sol: 63.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: The protein at 20 mg/ml was dissolved in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol, 2 mM DTT, and mixed 1:1 with well solution that was 20% PEG3350, 0.1 M bis-Tris, pH 6.0, 0.2 M ...Details: The protein at 20 mg/ml was dissolved in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5% glycerol, 2 mM DTT, and mixed 1:1 with well solution that was 20% PEG3350, 0.1 M bis-Tris, pH 6.0, 0.2 M NH4OAc, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 24173 / Num. obs: 24173 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rsym value: 0.09 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1192 / Rsym value: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FK9 Resolution: 1.8→24.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.103 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.082 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.203 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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