+Open data
-Basic information
Entry | Database: PDB / ID: 4i6j | ||||||
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Title | A ubiquitin ligase-substrate complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Circadian Clock / Ubiquitination / LRR / F-box / Photolyase fold / Periods / Nucleus | ||||||
Function / homology | Function and homology information regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity ...regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / entrainment of circadian clock by photoperiod / protein monoubiquitination / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / photoreceptor activity / ubiquitin-like ligase-substrate adaptor activity / response to light stimulus / phosphatase binding / protein K48-linked ubiquitination / post-translational protein modification / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / FAD binding / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / response to activity / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / nuclear receptor binding / regulation of circadian rhythm / Dectin-1 mediated noncanonical NF-kB signaling / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / kinase binding / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / circadian regulation of gene expression / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein destabilization / response to insulin / Degradation of beta-catenin by the destruction complex / circadian rhythm / Cyclin D associated events in G1 / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / G2/M transition of mitotic cell cycle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / beta-catenin binding / Interleukin-1 signaling / protein polyubiquitination / rhythmic process / protein import into nucleus / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Regulation of PLK1 Activity at G2/M Transition / glucose homeostasis / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / damaged DNA binding / chromatin remodeling / nuclear body / regulation of cell cycle / protein ubiquitination / nuclear speck / protein domain specific binding / negative regulation of DNA-templated transcription / centrosome / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.7 Å | ||||||
Authors | Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N. | ||||||
Citation | Journal: Nature / Year: 2013 Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket. Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6j.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6j.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 4i6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i6j_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 4i6j_full_validation.pdf.gz | 506.2 KB | Display | |
Data in XML | 4i6j_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 4i6j_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6j ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6j | 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: 61840.605 Da / Num. of mol.: 1 / Fragment: UNP residues 1-544 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194 |
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#2: Protein | Mass: 48772.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL3, FBL3A, FBXL3A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UKT7 |
#3: Protein | Mass: 18679.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63208 |
#4: 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: 2.56 Å3/Da / Density % sol: 51.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M ammonium citrate, 13-14% PEG3350 7% Acetonitrile, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2011 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 36840 / Num. obs: 36840 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 28.03 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.356 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement-SAD / Resolution: 2.7→47.522 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 29.04 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→47.522 Å
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Refine LS restraints |
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LS refinement shell |
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