+Open data
-Basic information
Entry | Database: PDB / ID: 4j2j | ||||||
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Title | Crystal structure of AXH domain complex with Capicua | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR / AXH domain / protein-protein interaction / Capicua | ||||||
Function / homology | Function and homology information poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory ...poly(G) binding / nuclear inclusion body / nuclear export / poly(U) RNA binding / social behavior / RNA processing / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / memory / nuclear matrix / nervous system development / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Song, J.-J. / Kim, E. | ||||||
Citation | Journal: Genes Dev. / Year: 2013 Title: Structural basis of protein complex formation and reconfiguration by polyglutamine disease protein Ataxin-1 and Capicua Authors: Kim, E. / Lu, H.-C. / Zoghbi, H.Y. / Song, J.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j2j.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j2j.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 4j2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j2j_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 4j2j_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 4j2j_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4j2j_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/4j2j ftp://data.pdbj.org/pub/pdb/validation_reports/j2/4j2j | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14296.744 Da / Num. of mol.: 3 / Fragment: AXH domain, UNP residues 562-688 / Mutation: I580M,I605M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54253 #2: Protein/peptide | Mass: 2366.712 Da / Num. of mol.: 3 / Fragment: UNP residues 28-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CIC / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RK0 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.45 % / Description: THE FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Calcium chloride, 24%(v/v) PEG3350, 4%(v/v) pentaerythritol ethoxylate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32436 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 52.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 15 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.43 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→43.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 65239.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. THE FILE CONTAINS FRIEDEL PAIRS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.7754 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→43.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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