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Yorodumi- PDB-5dzd: Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dzd | |||||||||
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Title | Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide | |||||||||
Components |
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Keywords | LIGASE/PROTEIN BINDING / structural genomics / Structural Genomics Consortium / SGC / LIGASE-PROTEIN BINDING complex | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å | |||||||||
Authors | Liu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide Authors: Liu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dzd.cif.gz | 36.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dzd.ent.gz | 23.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dzd_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 5dzd_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 5dzd_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 5dzd_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/5dzd ftp://data.pdbj.org/pub/pdb/validation_reports/dz/5dzd | HTTPS FTP |
-Related structure data
Related structure data | 2ysfS 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/peptide | Mass: 5503.151 Da / Num. of mol.: 2 / Fragment: UNP residues 324-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: custom / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-V2R-pRARE2 References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | Mass: 1359.589 Da / Num. of mol.: 2 / Fragment: UNP residues 327-338 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7 #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M sodium formate, 0.1 M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 22, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→37.24 Å / Num. obs: 16849 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Net I/σ(I): 42.7 / Num. measured all: 223544 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2YSF Resolution: 1.57→37.24 Å / SU B: 1.155 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078 Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. REFINEMENT RESTRAINTS FOR THE ACETYL AND AMIDE PROTECTED PEPTIDE TERMINI WERE PREPARED WITH JLIGAND. COOT WAS USED FOR INTERACTIVE MODEL ...Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. REFINEMENT RESTRAINTS FOR THE ACETYL AND AMIDE PROTECTED PEPTIDE TERMINI WERE PREPARED WITH JLIGAND. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.57→37.24 Å
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