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Yorodumi- PDB-3q4a: Crystal structure of the TPR domain of CHIP complexed with phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q4a | ||||||
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Title | Crystal structure of the TPR domain of CHIP complexed with phosphorylated Smad1 peptide | ||||||
Components |
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Keywords | LIGASE/TRANSCRIPTION / E3 ubiquitin ligase / LIGASE-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information mesodermal cell fate commitment / positive regulation of chaperone-mediated protein complex assembly / homomeric SMAD protein complex / Downregulation of TGF-beta receptor signaling / osteoblast fate commitment / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / SMAD protein complex / Regulation of TNFR1 signaling / Regulation of necroptotic cell death ...mesodermal cell fate commitment / positive regulation of chaperone-mediated protein complex assembly / homomeric SMAD protein complex / Downregulation of TGF-beta receptor signaling / osteoblast fate commitment / regulation of glucocorticoid metabolic process / Downregulation of ERBB2 signaling / SMAD protein complex / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / RUNX2 regulates bone development / heteromeric SMAD protein complex / Regulation of PTEN stability and activity / co-SMAD binding / Regulation of RUNX2 expression and activity / negative regulation of muscle cell differentiation / positive regulation of cartilage development / ubiquitin conjugating enzyme complex / DEAD/H-box RNA helicase binding / primary miRNA binding / positive regulation of ERAD pathway / positive regulation of mitophagy / positive regulation of smooth muscle cell apoptotic process / gamete generation / hindbrain development / cardiac conduction system development / primary miRNA processing / nuclear inclusion body / Antigen processing: Ubiquitination & Proteasome degradation / Signaling by BMP / misfolded protein binding / embryonic pattern specification / SMAD protein signal transduction / R-SMAD binding / I-SMAD binding / cartilage development / cellular response to misfolded protein / protein folding chaperone complex / Cardiogenesis / positive regulation of ubiquitin-protein transferase activity / nuclear inner membrane / cardiac muscle cell proliferation / ubiquitin-ubiquitin ligase activity / ureteric bud development / midbrain development / chaperone-mediated autophagy / homeostatic process / protein quality control for misfolded or incompletely synthesized proteins / BMP signaling pathway / TPR domain binding / positive regulation of sprouting angiogenesis / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / protein K63-linked ubiquitination / positive regulation of proteolysis / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / protein maturation / cellular response to organic cyclic compound / anatomical structure morphogenesis / protein autoubiquitination / positive regulation of osteoblast differentiation / ossification / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / heat shock protein binding / Hsp70 protein binding / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of miRNA transcription / positive regulation of protein ubiquitination / negative regulation of protein binding / response to ischemia / G protein-coupled receptor binding / kinase binding / Hsp90 protein binding / bone development / RING-type E3 ubiquitin transferase / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / MAPK cascade / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / cellular response to hypoxia / protein-macromolecule adaptor activity / protein-folding chaperone binding / cellular response to heat / DNA-binding transcription activator activity, RNA polymerase II-specific / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein stabilization / Ub-specific processing proteases / protein ubiquitination / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.542 Å | ||||||
Authors | Wang, L. / Chen, L. / Wu, J.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Molecular Mechanism of the Negative Regulation of Smad1/5 Protein by Carboxyl Terminus of Hsc70-interacting Protein (CHIP). Authors: Wang, L. / Liu, Y.T. / Hao, R. / Chen, L. / Chang, Z. / Wang, H.R. / Wang, Z.X. / Wu, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q4a.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q4a.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3q4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q4a_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 3q4a_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 3q4a_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3q4a_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/3q4a ftp://data.pdbj.org/pub/pdb/validation_reports/q4/3q4a | HTTPS FTP |
-Related structure data
Related structure data | 3q47C 3q49C 2c2lS C: citing same article (ref.) 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
#1: Protein | Mass: 15733.964 Da / Num. of mol.: 1 / Fragment: TPR domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stub1, Chip / Plasmid: pET-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9WUD1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Protein/peptide | Mass: 1185.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15797*PLUS |
#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: 1.92 Å3/Da / Density % sol: 36.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis-tris propane pH 7.0, 40% PEG MME 2000, 1% PEG MME 550, 50mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→33 Å / Num. all: 19828 / Num. obs: 19797 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 57.7 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 11.8 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C2L Resolution: 1.542→32.984 Å / SU ML: 0.16 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.234 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.542→32.984 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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