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Yorodumi- PDB-4htm: Mechanism of CREB Recognition and Coactivation by the CREB Regula... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4htm | ||||||
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Title | Mechanism of CREB Recognition and Coactivation by the CREB Regulated Transcriptional Coactivator CRTC2 | ||||||
Components | CREB-regulated transcription coactivator 2 | ||||||
Keywords | PROTEIN BINDING / alpha-helix / CREB binding / CREB | ||||||
Function / homology | Function and homology information : / positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / : / viral process / gluconeogenesis / Transcriptional activation of mitochondrial biogenesis / Circadian Clock / glucose homeostasis / protein homotetramerization ...: / positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / : / viral process / gluconeogenesis / Transcriptional activation of mitochondrial biogenesis / Circadian Clock / glucose homeostasis / protein homotetramerization / chromatin binding / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Luo, Q. / Viste, K. / Urday-Zaa, J.C. / Kumar, G.S. / Tsai, W.-W. / Talai, A. / Mayo, K. / Montminy, M. / Radhakrishnan, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Protein kinase N1, a cell inhibitor of Akt kinase, has a central role in quality control of germinal center formation Authors: Luo, Q. / Viste, K. / Urday-Zaa, J.C. / Kumar, G.S. / Tsai, W.-W. / Talai, A. / Mayo, K. / Montminy, M. / Radhakrishnan, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4htm.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4htm.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 4htm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/4htm ftp://data.pdbj.org/pub/pdb/validation_reports/ht/4htm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3952.445 Da / Num. of mol.: 1 / Fragment: CRTC2 CREB binding domain: unp residues 18-50 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q53ET0 | ||
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#2: Chemical | #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: 1.8 Å3/Da / Density % sol: 31.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, 150 mM zinc acetate, 3 M NaCl and 12% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 76 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. all: 19070 / Num. obs: 2595 / % possible obs: 99.4 % / Rsym value: 0.087 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 14.9 / Rsym value: 0.134 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→14.41 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.84 / SU B: 9.913 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 23.317 Å2
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Refinement step | Cycle: LAST / Resolution: 2→14.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 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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