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Yorodumi- PDB-5aiz: The PIAS-like coactivator Zmiz1 is a direct and selective cofacto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aiz | ||||||
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Title | The PIAS-like coactivator Zmiz1 is a direct and selective cofactor of Notch1 in T-cell development and leukemia | ||||||
Components | ZINC FINGER MIZ DOMAIN-CONTAINING PROTEIN 1 | ||||||
Keywords | ZINC-BINDING PROTEIN / PROTEIN | ||||||
Function / homology | Function and homology information : / transcription initiation-coupled chromatin remodeling => GO:0045815 / pyramidal neuron migration to cerebral cortex / : / regulation of protein sumoylation / vitellogenesis / SMAD protein signal transduction / positive regulation of T cell differentiation / artery morphogenesis / positive regulation of Notch signaling pathway ...: / transcription initiation-coupled chromatin remodeling => GO:0045815 / pyramidal neuron migration to cerebral cortex / : / regulation of protein sumoylation / vitellogenesis / SMAD protein signal transduction / positive regulation of T cell differentiation / artery morphogenesis / positive regulation of Notch signaling pathway / SMAD binding / androgen receptor signaling pathway / developmental growth / vasculogenesis / heart morphogenesis / transforming growth factor beta receptor signaling pathway / nuclear receptor coactivator activity / positive regulation of fibroblast proliferation / in utero embryonic development / transcription coactivator activity / intracellular membrane-bounded organelle / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Cho, H.J. / Murai, M. / Chiang, M. / Cierpicki, T. | ||||||
Citation | Journal: Immunity / Year: 2015 Title: The Pias-Like Coactivator Zmiz1 is a Direct and Selective Cofactor of Notch1 in T-Cell Development and Leukemia Authors: Cho, H.J. / Chiang, M. / Cierpicki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aiz.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aiz.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 5aiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aiz_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 5aiz_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 5aiz_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 5aiz_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5aiz ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5aiz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14227.590 Da / Num. of mol.: 1 / Fragment: TPR DOMAIN, UNP RESIDUES 1-118 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET32A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q9ULJ6 |
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#2: Chemical | ChemComp-UNX / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Sequence details | ZMIZ1 NTD WITH ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.67 % Description: THE STRUCTURE WAS SOLVED BY SAD PHASING AND AN INITIAL MODEL WAS GENERATED USING AN EARLY VERSION HKL3000 |
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Crystal grow | pH: 4.5 Details: 2.5 M SODIUM CHLORIDE, 0.2 M LITHIUM SULFATE AND 0.1 M SODIUM ACETATE PH4.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97928 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 11, 2012 |
Radiation | Monochromator: KOHZU MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 12677 / % possible obs: 98.2 % / Observed criterion σ(I): -2 / Redundancy: 10.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 32.85 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.65 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.7→35.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.946 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.103 / 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: 18.335 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35.46 Å
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