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Yorodumi- PDB-5fqd: Structural basis of Lenalidomide induced CK1a degradation by the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fqd | ||||||
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Title | Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase | ||||||
Components |
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Keywords | LIGASE / DNA BINDING | ||||||
Function / homology | Function and homology information negative regulation of monoatomic ion transmembrane transport / Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / positive regulation by virus of viral protein levels in host cell / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei ...negative regulation of monoatomic ion transmembrane transport / Activation of SMO / intermediate filament cytoskeleton organization / negative regulation of NLRP3 inflammasome complex assembly / cellular response to nutrient / positive regulation by virus of viral protein levels in host cell / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / beta-catenin destruction complex / Cul4-RING E3 ubiquitin ligase complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / UV-damage excision repair / Disassembly of the destruction complex and recruitment of AXIN to the membrane / biological process involved in interaction with symbiont / Maturation of nucleoprotein / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / positive regulation of Rho protein signal transduction / negative regulation of reproductive process / negative regulation of developmental process / Golgi organization / locomotory exploration behavior / cullin family protein binding / positive regulation of Wnt signaling pathway / viral release from host cell / ectopic germ cell programmed cell death / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / positive regulation of gluconeogenesis / positive regulation of TORC1 signaling / ciliary basal body / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / positive regulation of protein-containing complex assembly / DNA Damage Recognition in GG-NER / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / cilium / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / kinetochore / spindle / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Potential therapeutics for SARS / transmembrane transporter binding / chromosome, telomeric region / damaged DNA binding / cell surface receptor signaling pathway / protein ubiquitination / viral protein processing / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / protein-containing complex / DNA binding / extracellular space / extracellular exosome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Petzold, G. / Fischer, E.S. / Thoma, N.H. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Structural Basis of Lenalidomide-Induced Ck1Alpha Degradation by the Crl4(Crbn) Ubiquitin Ligase. Authors: Petzold, G. / Fischer, E.S. / Thoma, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fqd.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5fqd.ent.gz | 993.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/5fqd ftp://data.pdbj.org/pub/pdb/validation_reports/fq/5fqd | HTTPS FTP |
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-Related structure data
Related structure data | 3ei3S S: Starting model for refinement |
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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
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 95773.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q16531, ubiquitin-protein ligase #2: Protein | Mass: 48976.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q96SW2 #3: Protein | Mass: 39302.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P48729 |
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-Non-polymers , 3 types, 309 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Details: 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28161 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28161 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→65.3 Å / Num. obs: 140745 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 75.89 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EI3 Resolution: 2.45→65.3 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.289 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.212
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Displacement parameters | Biso mean: 96.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→65.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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