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- PDB-5cq2: Crystal Structure of tandem WW domains of ITCH in complex with TX... -
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Basic information
Entry | Database: PDB / ID: 5cq2 | |||||||||
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Title | Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide | |||||||||
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![]() | LIGASE / structural genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | ![]() 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 / cellular response to tumor cell / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / cellular response to oxidised low-density lipoprotein particle stimulus ...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 / cellular response to tumor cell / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / cellular response to oxidised low-density lipoprotein particle stimulus / CXCR chemokine receptor binding / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / negative regulation of cell division / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / 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 / ubiquitin-like protein ligase binding / protein monoubiquitination / ligase activity / protein K63-linked ubiquitination / platelet-derived growth factor receptor signaling pathway / The NLRP3 inflammasome / protein autoubiquitination / protein K48-linked ubiquitination / ribonucleoprotein complex binding / Purinergic signaling in leishmaniasis infection / response to glucose / response to mechanical stimulus / keratinocyte differentiation / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / response to progesterone / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / response to hydrogen peroxide / Regulation of necroptotic cell death / receptor internalization / Cytoprotection by HMOX1 / response to calcium ion / positive regulation of protein catabolic process / protein import into nucleus / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / response to estradiol / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of cell population proliferation / cell cortex / early endosome membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / inflammatory response / symbiont entry into host cell / positive regulation of apoptotic process / cell cycle / intracellular membrane-bounded organelle / innate immune response / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
![]() | ![]() Title: Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP. Authors: Liu, Y. / Lau, J. / Li, W. / Tempel, W. / Li, L. / Dong, A. / Narula, A. / Qin, S. / Min, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.9 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.9 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5df6C ![]() 4rre 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | As per the authors the biologically relevant macromolecular assembly is not applicable to this protein fragment |
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Components
#1: Protein | Mass: 10412.411 Da / Num. of mol.: 1 / Fragment: UNP residues 282-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||
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#2: Protein/peptide | Mass: 1359.589 Da / Num. of mol.: 2 / Fragment: UNP Residues 327-338 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) ![]() #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 30% PEG4000, 0.2 M magnesium chloride, 0.1 M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2013 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791829 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→45.86 Å / Num. obs: 24240 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 25.1 / Num. measured all: 172053 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RRE ![]() 4rre Resolution: 1.4→45.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.233 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / 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: 24.151 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→45.86 Å
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