+Open data
-Basic information
Entry | Database: PDB / ID: 4hxi | ||||||
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Title | Crystal structure of KLHL3/Cul3 complex | ||||||
Components |
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Keywords | PROTEIN BINDING / BTB-BACK / Protein-protein interaction | ||||||
Function / homology | Function and homology information distal tubule morphogenesis / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / monoatomic ion homeostasis / nuclear protein quality control by the ubiquitin-proteasome system / renal sodium ion absorption / regulation protein catabolic process at postsynapse / polar microtubule ...distal tubule morphogenesis / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / monoatomic ion homeostasis / nuclear protein quality control by the ubiquitin-proteasome system / renal sodium ion absorption / regulation protein catabolic process at postsynapse / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / potassium ion homeostasis / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / gastrulation / protein K48-linked ubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / protein autoubiquitination / RHOBTB2 GTPase cycle / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / macroautophagy / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / protein destabilization / mitotic spindle / Wnt signaling pathway / spindle pole / protein polyubiquitination / Regulation of RAS by GAPs / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / actin binding / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / protein ubiquitination / cytoskeleton / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / structural molecule activity / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.513 Å | ||||||
Authors | Ji, A.X. / Prive, G.G. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal structure of KLHL3 in complex with Cullin3. Authors: Ji, A.X. / Prive, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hxi.cif.gz | 228.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hxi.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/4hxi ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hxi | 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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Unit cell |
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-Components
#1: Protein | Mass: 31366.789 Da / Num. of mol.: 1 / Fragment: BTB-BACK / Mutation: K87A, K89A, K90A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL3, KIAA1129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH77 |
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#2: Protein | Mass: 45209.664 Da / Num. of mol.: 1 / Fragment: NTD / Mutation: K274R, I342R, L346D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13618 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ammonium tartrate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2012 |
Radiation | Monochromator: Double Si 111, Double Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. obs: 49265 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.5→3.56 Å / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.513→20 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 28.53 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.513→20 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.5498 Å / Origin y: -27.3909 Å / Origin z: -7.2261 Å
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Refinement TLS group | Selection details: all |