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- PDB-3i8e: Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i8e | ||||||
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Title | Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A | ||||||
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![]() | PROTEIN BINDING / DDB1 / WDR42A / H326 / DCAF8 / H-Box Motif / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Ubl conjugation pathway / WD repeat | ||||||
Function / homology | ![]() positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of gluconeogenesis / post-translational protein modification / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / 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 / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / mitochondrion / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T. / Robert, E.I. / Breugel, P.C.V. / Strubin, M. / Zheng, N. | ||||||
![]() | ![]() Title: A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery. Authors: Li, T. / Robert, E.I. / van Breugel, P.C. / Strubin, M. / Zheng, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 440.5 KB | Display | ![]() |
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PDB format | ![]() | 352.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 472.8 KB | Display | ![]() |
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Full document | ![]() | 545.1 KB | Display | |
Data in XML | ![]() | 80.3 KB | Display | |
Data in CIF | ![]() | 107.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i7hC ![]() 3i7kC ![]() 3i7lC ![]() 3i7nC ![]() 3i7oC ![]() 3i7pC ![]() 3i89C ![]() 3i8cC ![]() 2b5mS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 127399.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1441.633 Da / Num. of mol.: 2 / Fragment: Residues 153-165 / Source method: obtained synthetically / Source: (synth.) ![]() Sequence details | MUTATIONS OCCURRED DURING THE CLONING OF DDB1 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2008 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.4→49.15 Å / Num. all: 38723 / Num. obs: 35597 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 10.7 | |||||||||
Reflection shell | Resolution: 3.4→3.488 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2592 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2B5M Resolution: 3.4→49.15 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.804 / SU B: 91.559 / SU ML: 0.674 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.861 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.285 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→49.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.488 Å / 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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