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Yorodumi- PDB-4apf: Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4apf | ||||||
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Title | Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution | ||||||
Components |
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Keywords | CELL CYCLE / UBIQUITINATION / E3 LIGASE | ||||||
Function / homology | Function and homology information liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / mitotic metaphase chromosome alignment / ubiquitin ligase complex scaffold activity / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / sperm flagellum / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein autoubiquitination / protein K48-linked ubiquitination / gastrulation / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / mitotic spindle / Wnt signaling pathway / spindle pole / protein polyubiquitination / Regulation of RAS by GAPs / G1/S transition of mitotic cell cycle / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / postsynapse / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å | ||||||
Authors | Canning, P. / Cooper, C.D.O. / Krojer, T. / Vollmar, M. / Ugochukwu, E. / Muniz, J.R.C. / Ayinampudi, V. / Savitsky, P. / Arrowsmith, C.H. / Edwards, A.M. ...Canning, P. / Cooper, C.D.O. / Krojer, T. / Vollmar, M. / Ugochukwu, E. / Muniz, J.R.C. / Ayinampudi, V. / Savitsky, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Bullock, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases. Authors: Canning, P. / Cooper, C.D.O. / Krojer, T. / Murray, J.W. / Pike, A.C.W. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4apf.cif.gz | 251.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4apf.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 4apf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4apf_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 4apf_full_validation.pdf.gz | 441 KB | Display | |
Data in XML | 4apf_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 4apf_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4apf ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4apf | HTTPS FTP |
-Related 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: 34526.215 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN, BACK DOMAIN, RESIDUES 67-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 PRARE2 / References: UniProt: Q9NVR0 | ||
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#2: Protein | Mass: 45723.953 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 23-388 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3 / References: UniProt: Q13618 | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | I342R AND L346D ARE MUTATIONS ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.27 % / Description: STATISTICS DERIVED FROM THE NATIVE DATASET. |
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Crystal grow | Details: 0.12 M K CITRATE; 17% PEG 3350; 10% ETHYLENE GLYCOL; PH 6.5 BIS TRIS PROPANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9681 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9681 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 25043 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 127.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 3.1→35.88 Å / Cor.coef. Fo:Fc: 0.9483 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.489 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.297 Details: NUMBER OF LIBRARIES USED : 8 REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOM HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 115.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.756 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→35.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.23 Å / Total num. of bins used: 13
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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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