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Yorodumi- PDB-3hqm: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hqm | ||||||
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Title | Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-CiSBC2 | ||||||
Components |
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Keywords | PROTEIN BINDING / LIGASE / ubiquitin / E3 / SPOP / MATH / Ci / Nucleus / Ubl conjugation pathway / Developmental protein / DNA-binding / Metal-binding / Segmentation polarity protein / Zinc-finger | ||||||
Function / homology | Function and homology information N-HH ligand not bound to PTC receptor complex / Hedgehog signaling complex / Assembly of the CI containing complexes / Activation of CI / Activation of SMO / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Hedgehog 'off' state / cuticle pattern formation / Phosphorylation of CI ...N-HH ligand not bound to PTC receptor complex / Hedgehog signaling complex / Assembly of the CI containing complexes / Activation of CI / Activation of SMO / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Hedgehog 'off' state / cuticle pattern formation / Phosphorylation of CI / Phosphorylation of SMO / Nuclear CI is degraded / Assembly of the 'signalling complexes' / Ubiquitination and proteolysis of phosphorylated CI / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / heart formation / genital disc anterior/posterior pattern formation / compound eye morphogenesis / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / mucosal immune response / positive regulation of epithelial cell differentiation / segment polarity determination / cAMP response element binding protein binding / regulation of proteolysis / dendrite morphogenesis / Cul3-RING ubiquitin ligase complex / smoothened signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / molecular function inhibitor activity / negative regulation of hippo signaling / regulation of mitotic cell cycle / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hedgehog 'on' state / protein polyubiquitination / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Zhuang, M. / Schulman, B.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases. Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Seyedin, S.N. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hqm.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hqm.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hqm_validation.pdf.gz | 461.9 KB | Display | wwPDB validaton report |
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Full document | 3hqm_full_validation.pdf.gz | 463.9 KB | Display | |
Data in XML | 3hqm_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3hqm_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hqm ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hqm | HTTPS FTP |
-Related structure data
Related structure data | 3hqhSC 3hqiC 3hqlC 3hsvC 3htmC 3hu6C 3hveC 3ivqC 3ivvC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16485.932 Da / Num. of mol.: 2 / Fragment: UNP residues 28-166 / Mutation: D140G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791 #2: Protein/peptide | Mass: 1305.371 Da / Num. of mol.: 2 / Fragment: UNP residues 1356-1367 / Source method: obtained synthetically / References: UniProt: P19538 #3: Chemical | ChemComp-SO4 / #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: 2.3 Å3/Da / Density % sol: 46.47 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID |
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Detector | Date: Jun 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 31963 / Observed criterion σ(F): 0 / Redundancy: 2 % / Rsym value: 0.031 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 2996 / Rsym value: 0.102 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HQH Resolution: 1.74→25.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.13 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→25.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.8 Å / Num. reflection Rwork: 2067 / Total num. of bins used: 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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